PTAB Practice Toolkit: Inter Partes Review, Post-Grant Review, and Parallel Proceedings

By Casey Scott McKay · 2024-01-11

The Board is a second forum for validity, on a preponderance standard, with a fixed schedule and a hard bar, and the decision to use it is made in the first six months of a district court case or not at all. This toolkit runs a post-grant proceeding from the bar calculation through the final written decision and its consequences, and routes each stage to the Marksy documents that do the work. It covers the choice among inter partes review, post-grant review, and reexamination, the prior art search that should precede any filing decision, real party in interest analysis, ground selection under the all-or-nothing rule, petition anatomy and the expert declaration, the preliminary response and discretionary denial, the trial phase and its single deposition, amendment, and the estoppel that attaches at the end. It closes with the reading path, the authorities table, and the forms.

IP and Technology > Patent Litigation | Toolkit | Published 11 January 2024 - Updated 3 October 2025 | Casey Scott McKay - marksy.us

Summary. The Board is a second forum for validity, on a preponderance standard, with a fixed schedule and a hard bar, and the decision to use it is made in the first six months of a district court case or not at all. This toolkit runs a post-grant proceeding from the bar calculation through the final written decision and its consequences, and routes each stage to the Marksy documents that do the work. It covers the choice among inter partes review, post-grant review, and reexamination, the prior art search that should precede any filing decision, real party in interest analysis, ground selection under the all-or-nothing rule, petition anatomy and the expert declaration, the preliminary response and discretionary denial, the trial phase and its single deposition, amendment, and the estoppel that attaches at the end. It closes with the reading path, the authorities table, and the forms.

Keywords: inter partes review · post-grant review · ex parte reexamination · one-year bar · real party in interest · prior art search · ground selection · all-or-nothing institution · discretionary denial · petition drafting · expert declaration · motivation to combine · preliminary response · patent owner response · motion to amend · objective indicia · oral hearing · final written decision · estoppel · stay pending review

Start Here

Hollingbrook Systems was served eight months ago. Four facts sit on the desk and they are in tension.

The one-year bar runs in four months, which means the petition decision has to be made now and the petition drafted under pressure.

The prior art search has not been commissioned, so nobody knows whether art materially better than the examiner's exists.

The district court is a fast one with a trial date twenty months out, which is the strongest argument the patent owner has against institution.

And the company's best invalidity argument may be an on-sale bar based on a product the plaintiff itself shipped years before filing — which cannot be raised at the Board at all.

Four facts, one decision, and a common error: treating the Board as a default rather than as one option whose availability depends on what the invalidity case is made of.

This toolkit answers three questions.

Is the Board available, and is it the right forum? Only patents and printed publications under two statutory grounds, and only within the bar.
What does the petition have to contain? Everything, because there is no discovery to fill gaps and no appeal from a denial of institution.
What does losing cost? Estoppel on grounds raised or reasonably available, which is priced against what stays behind in district court.

If you read only one thing, read The Second Look. It explains what the proceeding is and why it changed settlement economics permanently.

Choosing the Proceeding

Inter partes review. 35 U.S.C. § 311. Available nine months after issuance for patents subject to post-grant review, and not later than one year after service of an infringement complaint on the petitioner, a real party in interest, or a privy. 35 U.S.C. § 315(b). Grounds limited to novelty and obviousness under 35 U.S.C. § 102 and 35 U.S.C. § 103, and only on patents and printed publications.

Post-grant review. 35 U.S.C. § 321. Available within nine months of issuance for patents with an effective filing date on or after 16 March 2013. Permits every invalidity ground, including eligibility under 35 U.S.C. § 101 and the disclosure grounds under 35 U.S.C. § 112. Broader, and its estoppel is correspondingly broader.

Ex parte reexamination. 35 U.S.C. § 302. Filable at any time, on a substantial new question of patentability, with no statutory estoppel and no requirement to identify the real party. The requester then has essentially no role, the proceeding has no deadline, and the patent owner amends and argues freely.

Doing nothing at the Board. Correct for many defendants. Where the best arguments are eligibility, indefiniteness, an on-sale bar, or a physical product as prior art, the money belongs in district court.

Hollingbrook's on-sale argument falls in that category, and it is a reason to weight the estoppel inventory carefully rather than a reason to skip the Board.

The Bar and the Real Decision Date

Calendar the one-year date from service, not from filing of the complaint and not from an amended complaint.

Check whether any privy or real party in interest was served earlier. Service on a party at whose behest the petition would be filed starts the clock for the petitioner. This defeats petitions on grounds unrelated to the merits and it is the most avoidable failure in the practice.

Set the real decision date at month six. A competent petition needs a four-to-six week search, an expert engaged and briefed, charts built element by element, and a drafting cycle. Working backward, the decision cannot wait.

Note the district court trial date. It is the strongest argument against institution and it argues for filing early rather than late.

Hollingbrook's problem. Eight months elapsed, four remain, and no search has been run. The honest options are to commission the search immediately and accept a compressed drafting cycle, or to conclude that a petition drafted in six weeks against a fast trial date will lose on institution and to spend the money in district court instead. The second is frequently the right answer and it is rarely the one clients want.

The Search and the Filing Decision

Read the file wrapper first. The references the examiner cited are on the face of the patent and the office actions show what the examiner thought they taught. Art already considered invites discretionary denial and rarely persuades.

Identify the amendment that produced allowance. That limitation is the point of novelty and it defines the search.

Commission the search against that limitation, not against the field.

Prioritize what examiners search poorly. Non-patent literature, conference proceedings, standards contributions, foreign patent documents, product manuals, and theses.

Verify public availability dates. A printed publication must have been publicly accessible before the critical date, and a conference paper or standards contribution requires proof of when and how. 35 U.S.C. § 102.

Ask for a materiality assessment, not a reference list. The question is whether the art is materially better than what the examiner saw, and only the searcher who read both can answer it.

Then decide. If the art is not materially better, do not file. Seeming weak is not a ground.

Real Parties in Interest

Do the analysis in writing before drafting. Incomplete disclosure terminates petitions on grounds having nothing to do with the merits.

The test is functional. At whose behest is the petition filed? Consider the corporate parent, subsidiaries and affiliates, indemnitors and indemnitees, suppliers who agreed to defend, customers under an indemnity, insurers funding the defense, joint defense group members, and anyone with control over petition strategy.

Two consequences of getting it wrong. Termination for incomplete identification, and importation of a one-year bar from a complaint served on an unnamed party earlier.

List related matters completely. Every district court action, every other Office proceeding touching the patent or its family, and every related application.

Deliverable. A memorandum listing each candidate entity, the relationship, and the conclusion, signed off by someone who knows the corporate structure and the indemnity arrangements.

Ground Selection

Institution is all or nothing. 35 U.S.C. § 314. The Board institutes on every challenged claim and every ground or on none, which makes a weak ground a threat to the strong ones.

Rank candidates by the strength of the weakest element mapping, and cut everything below the line.

Prefer anticipation where a single reference genuinely discloses every limitation arranged as claimed, because it avoids the motivation-to-combine problem entirely.

Prefer two-reference combinations over three-reference stacks.

Three strong grounds beat six mixed ones. Petitions are rejected for sprawl more often than for weakness, and the word limit means cutting grounds buys words for the ones that remain.

Justify parallel petitions in writing if more than one is filed against the same patent, ranked in order of preference. Unexplained parallel petitions are routinely reduced to one.

Check joinder where a co-defendant has already filed. 35 U.S.C. § 315(c) permits a party otherwise barred to join an instituted proceeding, usually on the existing grounds.

The Estoppel Inventory

What attaches. On a final written decision, the petitioner and its real parties in interest and privies may not assert in district court, at the Board, or at the Commission that a claim is invalid on any ground raised or that reasonably could have been raised. 35 U.S.C. § 315(e).

"Reasonably could have raised" is broad. It reaches art a reasonably diligent search would have found, which means holding back a fourth reference generally does not preserve it.

It attaches per claim on the final written decision. Claims never instituted on generally carry no estoppel because there is no decision as to them.

What survives regardless. Eligibility under 35 U.S.C. § 101. Every ground under 35 U.S.C. § 112. Prior public use and on-sale activity not documented in a publication. A physical product as prior art. Inequitable conduct. And non-infringement, which the Board never touches.

The deliverable. A two-column memorandum: grounds going to the Board, grounds staying in district court. A defendant whose invalidity case is entirely documentary bets that case on the petition; one with a strong on-sale bar and a section 112 problem loses little by filing.

The Petition

The petition is the entire case. No amendment, no discovery to fill gaps, and no appeal from a denial of institution.

Mandatory notices. Real parties in interest, related matters, lead and back-up counsel, and service information.

Grounds for standing. The certification that the petitioner is neither barred nor estopped.

Statement of the precise relief requested. The ground table in prose — which claims, which statutory basis, which references — visible in half a page.

Technology background, kept short. A page of orientation. Five pages consume the word budget the charts need.

Level of ordinary skill, stated explicitly with expert support, because every obviousness question is answered from that person's perspective.

Claim construction for contested terms only. A petition construing eleven terms invites eleven disputes and will lose most without benefit. The Board applies the same standard as the district court, which means positions taken here travel.

One section per ground, self-contained, with element-by-element charts carrying pin citations to column and line or paragraph number.

The motivation to combine, specifically. Grounded in the references, in the knowledge of the skilled artisan, or in the problem being solved, with a reasonable expectation of success. Shared field of endeavor is not a reason and it is the reason given most often.

Teaching away addressed where the reference contains discouraging language.

Objective indicia addressed where foreseeable, because a reply constrained against new argument is a poor place to meet them.

Dependent claims charted individually.

The Expert Declaration

It does what the petition cannot. Establishes what a person of ordinary skill would have understood and why.

Three failure modes. A declaration that tracks the petition verbatim, which is discounted. A declaration that asserts conclusions without the reasoning path. And an expert from an adjacent field rather than the actual one, who is easier to impeach.

Brief the expert on the file wrapper before drafting, because discovering at deposition that the expert never read what the applicant argued is a credibility problem the record keeps.

Prepare for hindsight questioning, which is the most productive line available to a patent owner: how were the references selected, and what would have led a skilled artisan to this combination without knowing the patent.

The deposition is the whole of discovery in a paper proceeding, and the transcript is what the panel reads. Fed. R. Evid. 702.

The Preliminary Response and Discretionary Denial

It is optional, filed before institution, and it is the only chance to stop the proceeding entirely.

Lead with procedure where available. An unnamed real party in interest, a bar running from a privy's service date, or a defective certification is cleaner than the merits.

Build the discretionary denial argument from the district court record. Trial date, investment by the parties and the court, overlap in issues, whether the petitioner is the district court defendant, the petitioner's delay in filing, and the merits strength. This argument is strongest against a late petition in a fast district.

Argue previously presented art where the petition recycles references already before the examiner.

Attack the combination rather than the references. Petitions fail on motivation far more often than on what a reference discloses.

Hold the objective indicia and the detailed technical rebuttal for the post-institution response unless decisive on their face, because a preliminary response that fronts the whole defense and loses institution anyway has previewed everything.

Institution is generally not appealable, which makes the petition and the preliminary response the whole of the argument. 35 U.S.C. § 314.

The Trial Phase

The clock. A final written decision within twelve months of institution, extendable by six for good cause. 35 U.S.C. § 316. The Board meets it.

The sequence. Patent owner response with declaration; petitioner reply; patent owner sur-reply; depositions of declarants; oral hearing; decision.

Discovery is routine cross-examination plus additional discovery only in the interests of justice. There is no document production of the kind district court litigation involves.

The reply is constrained. New evidence and new theories are excluded, and petitioners lose ground routinely by reserving the real argument for reply.

The patent owner's best material. Teaching away in the reference's own language, a modification that would defeat the primary reference's purpose, hindsight in the combination rationale, and objective indicia with a nexus to the claimed features.

Claim construction consistency with the district court, in both directions.

The oral hearing is about an hour per side before a technically trained panel that has read everything. Demonstratives may not contain new argument, and the panel goes directly to the weakest point.

Amendment and Outcomes

Motions to amend are available under 35 U.S.C. § 316(d) and succeed at a low rate. Substitute claims must be narrower, supported by the original disclosure, and patentable over the art of record, and the compressed schedule leaves little room to build support. Treat amendment as a fallback.

All claims cancelled ends the matter as to that patent, subject to pending continuations and the certificate issuing.

Some claims cancelled leaves an infringement case on the survivors and may change the damages analysis if the cancelled claims covered a different product or period.

All claims survive. The patent is materially stronger — the petitioner is estopped on the documentary grounds, the presumption of validity reads differently to a jury, and settlement value moves against the defendant. This is the real downside of filing and it should be described before the decision.

Institution denied produces no estoppel and no decision, and a discretionary denial is not a merits ruling. Describing it to a client as one creates a problem when the district court case continues.

Appeal. 35 U.S.C. § 141. Legal conclusions reviewed without deference, factual findings for substantial evidence. What a reference teaches is factual, which makes reversal on the core of an obviousness determination difficult; appeals succeed more often on construction and procedure.

Settlement and termination before a final written decision generally avoids estoppel, which is why a large share of these proceedings never reach decision.

Coordinating With the District Court

Move to stay on filing, and again after institution. The first motion usually fails and costs little; the second succeeds far more often, and having preserved the request keeps the record clean.

Maintain a running map of grounds — at the Board, in district court, and estopped on a final written decision. This is what prevents an estopped ground from appearing in an expert report.

Keep claim construction positions consistent.

Use one expert across both proceedings, or accept the risk. Two experts whose positions differ hand the other side a cross-examination it did not have to build.

Preserve documents notwithstanding a stay.

Watch the Commission schedule where a section 337 investigation is pending, because it does not wait and estoppel reaches it.

Reassess settlement at each milestone — filing, institution, and the close of briefing each change the risk profile materially.

Reading the Numbers Correctly

Statistics about the Board circulate constantly and they are misread in both directions.

Institution rates move with discretionary denial practice rather than with the merits, which means a rate cited from three years ago describes a different regime.

Outcome rates among instituted proceedings show a substantial majority resulting in at least one claim cancelled and a large fraction in all challenged claims cancelled. These are quoted as proof that the Board is hostile to patents.

They are selection effects. Petitions are filed by parties that found art they believe is materially better than the examiner's, after a search costing real money, against patents already asserted in litigation. Cases that settle disappear from the denominator. Patents with strong prosecution records and thorough examination are rarely petitioned at all. The population reaching a final written decision is the subset a motivated adversary selected as weakest.

What follows for a petitioner. The rates say nothing about whether this petition will succeed. The search in the previous section does.

What follows for a patent owner. The defenses that matter are built during prosecution, not at the Board: a record showing the examiner considered the closest art, a claim set with meaningful dependent claims, and a specification supporting the constructions the claims will need. See Patent Prosecution Toolkit.

What follows for a client conversation. Do not describe a filing as likely to succeed because of aggregate statistics, and do not describe a denial as vindication. Both misstate what the numbers mean.

How the Rules Have Moved

Anyone reading guidance more than a few years old should know which parts have changed.

Claim construction. The Board originally applied the broadest reasonable interpretation, producing the uncomfortable result that a claim could be cancelled on a construction broader than the district court would adopt. The standard was changed by rule to match the district court's, and the inconsistency largely disappeared.

Partial institution. The Board originally instituted claim by claim and ground by ground, trying the strong ones and discarding the weak. The Supreme Court held the statute does not permit that, and the all-or-nothing rule followed — which reshaped petition drafting overnight, because a makeweight ground now endangers the good ones.

The burden on a motion to amend moved to the petitioner to show the substitute claims unpatentable, and amendment success rates rose from negligible to merely low.

Discretionary denial practice has been the most volatile area, with the weight given to a parallel trial date, to a petitioner's stipulation about what it will not argue in district court, and to previously presented art all shifting with changes in leadership at the Office. Guidance on this specific question ages fastest.

What is stable. The statutory core: patents and printed publications only, the one-year bar, the preponderance standard, the twelve-month decision, and estoppel on grounds raised or reasonably available. A practitioner who holds those five can absorb the rest.

Hollingbrook's Decision

Eight months elapsed, four remaining, no search commissioned, a fast trial date, and a strong on-sale argument that cannot be raised at the Board. Here is the analysis.

Commission the search this week, aimed at the limitation the examiner allowed over. Four to six weeks. Without it there is no filing decision to make, only a guess.

Run the real party in interest memorandum in parallel. If any indemnitor or supplier was served earlier, the bar may already have run and the whole question is moot.

Model the discretionary denial risk honestly. A petition filed at month eleven, in a district with a trial date twenty months out, faces the strongest version of the parallel-proceedings argument. The final written decision would arrive around month thirty-four from service; the trial around month twenty. That is the fact pattern the doctrine was written for.

Consider the stipulation. A petitioner that stipulates not to pursue in district court the grounds it raises at the Board reduces the overlap and has historically improved institution odds. Whether it is worth giving up depends entirely on the estoppel inventory.

Price the estoppel. The on-sale bar survives a final written decision regardless. So does any section 112 argument. If those are the strongest grounds, the documentary case is not the whole case and a petition costs little in preserved arguments.

The likely recommendation. If the search returns art materially better than the examiner's, file at month ten with a stipulation and move to stay immediately. If it does not, do not file — spend the money on the on-sale defense, which is the strongest argument available and which the Board could never have heard.

And fix the process. A defendant that reaches month eight without a search has already lost most of its options. The trigger should be service, not the approach of the bar.

What It Costs

The search. Modest, front-loaded, and it buys the filing decision. Skipping it to save money is the most expensive economy available.

The petition. Drafting, charting, and the expert declaration. Substantial, and it purchases a decision rather than a result.

The preliminary response. A fraction of the petition, and for a patent owner it has the highest expected value of any filing in the proceeding because it is the only one that can end the matter outright.

The trial phase. Response or reply, one deposition per declarant, and the hearing. Meaningfully cheaper than the equivalent phase of district court litigation, which is the proceeding's principal attraction.

The appeal, where taken.

Against what. The cost of litigating invalidity to a jury verdict on a clear and convincing standard, plus the settlement value of a patent that has not been tested. For a defendant facing a campaign or a core-product assertion, the ratio strongly favors filing where the art supports it.

Staffing. A drafting lawyer who knows the technology, a second reader who has not seen the art before, and an expert who writes their own analysis. The second reader matters more than teams expect, because petitions fail on gaps invisible to whoever assembled the argument.

Fifteen Failure Modes

Filing late. The most common cause of denial having nothing to do with the art.

Never commissioning the search, so the filing decision is an instinct rather than a finding.

Filing on the examiner's art. References already on the face of the patent were considered, rejected as insufficient, and are now being offered again.

Incomplete real party in interest disclosure, which terminates petitions and imports bars.

Too many grounds. All-or-nothing institution makes the marginal ground expensive.

Charts that quote without mapping. A block quotation beside a limitation is not an analysis.

Motivation to combine by shared field, which the Board rejects in decision after decision.

A declaration that mirrors the petition, discounted, and the discount usually falls on the ground that needed the expert most.

An expert who has not read the file wrapper, discovered at deposition, on the record.

Ignoring objective indicia and finding the reply constrained against new argument.

New argument in reply, excluded, and the ground it was meant to save fails.

Eleven claim construction positions, inviting eleven disputes and losing most without benefit.

Inconsistent constructions across the Board and the district court, which each side does to itself at least once.

Planning on amendment, which rarely carries a defense.

Treating a stay denial as final rather than renewing after institution.

And one framing error. Describing a discretionary denial to a client as a merits win. It is not, and the client finds out when the district court case continues.

The Patent Owner's Program

Everything a patent owner can do about the Board it does years earlier, during prosecution and portfolio management.

Build a thorough examination record. A file wrapper showing the examiner considered the closest art, with substantive rejections overcome on the merits, is the strongest defense against both the merits and the discretionary denial analysis.

Disclose broadly. Art submitted under 37 C.F.R. § 1.56 and considered by the examiner is art a petitioner cannot use cleanly, because it invites the previously-presented-art argument.

Draft meaningful dependent claims. A patent whose independent claim falls and whose dependents add nothing loses everything at once. Dependents that add real, separately supported limitations frequently survive, and surviving claims still support an infringement case and still carry estoppel against the petitioner.

Keep a continuation pending. Where claims are cancelled, a live continuation permits new claims drafted around the art, carrying the original priority date. This is the closest thing to insurance available against a post-grant proceeding, and it costs a filing fee at each issuance.

Consider reissue where a defect is known. 35 U.S.C. § 251. Broadening reissue is available only within two years of grant, and reissue opens the claims to fresh examination on every ground — which is a real cost.

Model the exposure per family in the portfolio inventory: the strength of the record, whether better art is known to exist, and whether the family would survive a petition. That field converts a portfolio review into a risk assessment.

Sue in a fast district where venue permits, because a near-term trial date is the strongest available argument against institution and it is the one variable a patent owner controls at filing.

And be realistic in valuation. A patent that would not survive a petition is worth less than its claims suggest, and a buyer's counsel will run the same analysis before pricing the portfolio. That is uncomfortable to hear and it is better heard from the company's own lawyer than from an acquirer's.

A Suggested Reading Path

If you are deciding whether to file:

If you are the patent owner:

For the parallel district court case:

Primary Authorities

| Authority | Proposition | |---|---| | 35 U.S.C. § 311 | Inter partes review; scope | | 35 U.S.C. § 314 | Institution threshold; non-appealability | | 35 U.S.C. § 315(b) | One-year bar | | 35 U.S.C. § 315(c) | Joinder | | 35 U.S.C. § 315(e) | Estoppel | | 35 U.S.C. § 316 | Conduct; twelve-month decision; amendment | | 35 U.S.C. § 321 | Post-grant review | | 35 U.S.C. § 302 | Ex parte reexamination | | 35 U.S.C. § 101 | Not available in inter partes review | | 35 U.S.C. § 102 | Novelty; available ground | | 35 U.S.C. § 103 | Obviousness; available ground | | 35 U.S.C. § 112 | Not available; survives estoppel | | 35 U.S.C. § 141 | Appeal to the Federal Circuit | | 35 U.S.C. § 251 | Reissue; the patent owner's tool | | 35 U.S.C. § 282 | Presumption of validity; absent at the Board | | 37 C.F.R. § 42.100 | Rules for inter partes review | | 37 C.F.R. § 1.56 | Duty of disclosure in co-pending applications | | Fed. R. Evid. 702 | Expert testimony |

Forms and Templates

The Cease and Desist Template is where the one-year clock frequently begins in substance, because a demand letter starts the assessment even though the bar runs from service of a complaint — and a recipient that calendars the letter is a recipient with time to search. The Portfolio Inventory Template should record, for each patent the company owns, its exposure to a petition: the strength of the prosecution record, whether better art is known to exist, and whether continuations remain pending. The License Agreement Template matters because settlement before a final written decision generally avoids estoppel, which makes a licence the cheapest available exit. The Office Action Response Template belongs here for the patent owner: the prosecution record a petition attacks was written under it, and a thorough examination record is the best defense against a discretionary denial argument going the wrong way.

Related Toolkits and Checklists

For the district court case running alongside, the Patent Litigation Toolkit supplies the sequence and the stay strategy. For the construction positions that travel between forums, the Claim Construction Toolkit. For the defense economics that determine whether a petition is worth filing, the Patent Assertion Defense Toolkit. For the patent owner's perspective on building a record that survives, the Patent Prosecution Toolkit. And for the doctrine, the Patent Fundamentals Toolkit.