Ex Parte Reexamination vs. IPR in 2026: Cost, Estoppel, Timing & the Pre-Order Paper

Choosing between ex parte reexamination and inter partes review (IPR) can affect patent litigation strategy, legal expenses, and the invalidity arguments available later. Both procedures allow the United States Patent and Trademark Office (USPTO) to reconsider issued patent claims, but they operate differently.

The ex parte reexamination vs IPR decision has become especially relevant in 2026. Ex parte reexamination offers an examination-based process with limited requester participation, while IPR provides an adversarial proceeding before the Patent Trial and Appeal Board (PTAB).

A new April 2026 procedure also allows patent owners to submit a pre-order paper before the USPTO determines whether a substantial new question of patentability exists in qualifying reexamination requests.

For challengers, the decision involves cost, timing, participation rights, and estoppel. For patent owners, understanding the available responses is equally important.

This guide compares both procedures and explains when each may fit a particular patent dispute.

Key Takeaways

• Ex parte reexamination and IPR follow different procedures. Reexamination is examination-based, while IPR is an adversarial PTAB proceeding.
• USPTO fees differ significantly. Large-entity ex parte reexamination fees are $13,545 for non-streamlined requests and $6,775 for streamlined requests. IPR requires a $23,750 request fee plus a $28,125 post-institution fee for up to 20 claims.
• Estoppel is a major distinction. IPR petitioners face statutory estoppel under 35 U.S.C. 315(e), while ex parte reexamination has no equivalent statutory provision.
• Patent owners have a new response opportunity. For qualifying reexamination requests filed on or after April 5, 2026, owners may submit a pre-order paper of up to 30 pages, without a fee, within 30 days of service.
• Neither procedure guarantees review. Reexamination requires a substantial new question of patentability, while IPR has a different institution standard and applicable discretionary considerations.
• The appropriate route depends on the dispute. Prior art, litigation status, available budget, participation needs, and future invalidity defenses should guide the decision.

What Is the Difference Between Ex Parte Reexamination and IPR?

Both procedures allow issued patent claims to be challenged using patents or printed publications. Their principal difference is how the USPTO conducts the proceeding and how much involvement the challenger retains.

Ex parte reexamination operates through the USPTO’s examination process. A requester identifies prior art allegedly raising a substantial new question of patentability (SNQ). If the Office orders reexamination, the process generally proceeds between the patent owner and the USPTO, with limited third-party requester participation.

IPR is a trial-like administrative proceeding. The petitioner identifies challenged claims and presents invalidity grounds to the PTAB. The patent owner can respond, and an instituted proceeding may involve declarations, discovery, motions, briefing, and an oral hearing.

Comparison factor	Ex parte reexamination	Inter partes review (IPR)
Who may file?	Any person, including the patent owner	A person who is not the patent owner
Legal authority	35 U.S.C. 302 to 307	35 U.S.C. 311 to 319
Available grounds	Patentability questions based on patents or printed publications	Sections 102 and 103, based on patents or printed publications
Initial standard	Substantial new question of patentability	Reasonable likelihood of prevailing on at least one challenged claim
Proceeding type	USPTO examination	Adversarial PTAB proceeding
Challenger participation	Generally limited after the initial request stage	Active participation throughout the proceeding
Patent owner options	Pre-order paper for qualifying requests, responses, and permitted amendments	Preliminary response, substantive defense, and permitted motions
Statutory petitioner estoppel	No equivalent to 35 U.S.C. 315(e)	Estoppel under 35 U.S.C. 315(e)
Timing	Special dispatch required	Statutory institution and final decision deadlines
Discretionary considerations	Includes 35 U.S.C. 325(d)	Includes 35 U.S.C. 325(d) and other applicable considerations

For foundational definitions, see the reexamination glossary and the detailed inter partes review guide.

The key strategic difference is control. IPR allows a petitioner to participate actively, while ex parte reexamination generally gives the requester less influence after the initial stages.

Who Can File Each Procedure, and What Grounds Are Available?

Eligibility and available invalidity grounds should be evaluated before comparing filing fees.

Under 35 U.S.C. 302, any person, including the patent owner, may request ex parte reexamination based on qualifying patents or printed publications.

The request must identify the relevant prior art and explain how it raises a substantial new question of patentability affecting the patent claims.

Under 35 U.S.C. 311, an IPR petition may be filed by a person who is not the patent owner. The challenge must rely on anticipation or obviousness under Sections 102 or 103, using patents or printed publications.

IPR also carries additional filing restrictions.

For example, 35 U.S.C. 315(b) generally prevents institution when an IPR petition is filed more than one year after the petitioner, real party in interest, or privy was served with a complaint alleging infringement, subject to statutory exceptions.

Companies already involved in litigation should review service dates and related-party relationships before preparing an IPR petition.

What prior art should challengers evaluate?

The analysis should begin with the challenged patent claims and the available evidence.

Important questions include:

• Do the references qualify as patents or printed publications?
• Were the references publicly available early enough to constitute applicable prior art?
• Does each reference address the relevant claim limitations?
• Is the anticipation or obviousness argument properly supported?
• Did the USPTO previously consider the same references or substantially similar arguments?

The distinction between available proceedings matters because the broader grounds for patent invalidity are not all available through IPR or ex parte reexamination.

A challenge involving issues outside the permitted grounds may require a different procedural strategy.

How Does the Substantial New Question Standard Compare With IPR Institution?

Ex parte reexamination and IPR apply different thresholds for initiating substantive review.

Under 35 U.S.C. 303, the USPTO determines whether a request raises a substantial new question of patentability affecting at least one patent claim.

An SNQ determination does not establish that the patent is invalid. It means the identified prior art presents a sufficiently substantial patentability issue to justify further examination.

The Office may consider previously cited patents or printed publications where the statutory requirements are satisfied.

IPR applies the standard in 35 U.S.C. 314. Institution requires a determination that there is a reasonable likelihood the petitioner would prevail concerning at least one challenged claim.

An IPR petition must therefore present a detailed claim-specific challenge supported by appropriate evidence and legal reasoning.

What happens when the prior art was previously considered?

Under 35 U.S.C. 325(d), the USPTO may decline to institute or order a proceeding when the same or substantially the same prior art or arguments were previously presented to the Office.

This provision applies to both procedures.

Consequently, challengers should examine the patent’s prosecution history and relevant earlier proceedings.

A strong filing should explain the significance of the identified references and address how the proposed challenge differs from issues previously considered.

How Much Does Ex Parte Reexamination vs IPR Cost in 2026?

Official USPTO fees are one of the clearest differences between the two procedures.

The following figures reflect the specified large-entity charges in the USPTO fee schedule.

USPTO fee comparison

USPTO fee category	Ex parte reexamination	IPR
Non-streamlined request	$13,545	Not applicable
Streamlined request	$6,775	Not applicable
IPR request fee, up to 20 claims	Not applicable	$23,750
IPR post-institution fee, up to 20 claims	Not applicable	$28,125
Combined listed IPR request and post-institution fees	Not applicable	$51,875

These figures represent USPTO large-entity fees, not total legal expenses. Additional applicable fees, attorney fees, expert expenses, and other professional costs are excluded.

The streamlined reexamination fee is available only when the request satisfies the applicable USPTO requirements. A requester should confirm eligibility rather than assuming the lower fee applies.

What determines the total cost?

For ex parte reexamination, significant cost drivers include prior-art searching, technical analysis, claim mapping, request preparation, and prosecution-history review.

IPR often requires additional adversarial work. Potential expenses include expert declarations, discovery, motions, briefing, and hearing preparation.

The patent owner’s defense costs also vary.

A reexamination response may require detailed technical arguments and evaluation of potential claim amendments. An IPR defense may involve expert evidence, procedural motions, and extensive written submissions.

When comparing attorney proposals, request separate estimates for USPTO fees, initial preparation, potential later proceedings, and expert involvement.

The lowest filing fee does not necessarily produce the lowest total expense. The more useful comparison is the anticipated legal work required by the specific challenge.

What Is the Ex Parte Reexamination Timeline Compared With IPR?

The ex parte reexamination timeline differs from IPR because the procedures follow separate statutory frameworks.

Under 35 U.S.C. 303(a), the USPTO generally must determine whether an SNQ exists within three months after a reexamination request is filed.

If reexamination is ordered, 35 U.S.C. 305 requires the proceeding to be conducted with special dispatch.

However, special dispatch does not guarantee completion by a particular date. The overall duration depends on the issues raised, patent owner responses, amendments, and procedural developments.

IPR provides more defined statutory milestones.

Under 35 U.S.C. 313 and applicable rules, the patent owner generally has three months after the notice of filing date to submit a preliminary response.

Section 314(b) generally requires an institution determination within three months after receipt of the preliminary response or the deadline for that response.

Following institution, 35 U.S.C. 316(a)(11) generally requires a final written determination within one year, subject to a possible extension of up to six months for good cause and applicable adjustments for joinder.

Effective October 20, 2025, the USPTO Director became responsible for deciding institution of all IPR and post-grant review petitions under revised procedures.

How does pending litigation affect timing?

Filing either proceeding does not automatically pause related federal court litigation.

A district court may consider a stay, but the decision depends on the circumstances, including the litigation’s progress and the relationship between the issues.

Companies comparing the PTAB vs. federal court should evaluate the USPTO deadlines alongside discovery schedules, claim construction, and potential trial dates.

The objective is to select a procedure that supports the overall litigation strategy, not simply one with a preferred scheduling framework.

What Is the New Ex Parte Reexamination Pre-Order Paper in 2026?

The ex parte reexamination pre-order paper is an important procedural development for patent owners.

According to the USPTO’s April 2026 Official Gazette notice, patent owners may submit a paper addressing the substantial new question determination for reexamination requests filed on or after April 5, 2026.

This provides an opportunity to address the identified patentability question before the Office decides whether to order reexamination.

What are the filing requirements?

The notice establishes the following requirements:

• Applicable requests: Ex parte reexamination requests filed on or after April 5, 2026.
• Filing deadline: Within 30 days of service of the request.
• Page limit: Up to 30 pages.
• USPTO filing fee: No fee.
• Purpose: Address whether the cited teachings establish a substantial new question of patentability.

The 30-day deadline is not extendable under the notice.

A supporting declaration may be submitted without counting toward the paper’s page limit, but substantive arguments must appear in the paper rather than being incorporated by reference.

What should the patent owner include?

The submission should focus on the references and teachings relied upon in the request.

Counsel should examine the prosecution record, identify the specific patentability questions presented, and explain why those questions may not satisfy the SNQ standard.

The notice also distinguishes the SNQ analysis from discretionary considerations under Section 325(d). The pre-order paper should not address whether the Office should exercise Section 325(d) discretion.

Can a requester respond?

Third-party requesters generally cannot submit a reply to the patent owner’s pre-order paper.

Limited exceptions may apply under the notice, including circumstances involving alleged material misrepresentations or improper arguments that interfere with the SNQ determination.

A requester seeking an exception must follow the applicable petition requirements.

The new procedure makes prompt review important for patent owners and reinforces the need for challengers to prepare complete initial requests.

It does not guarantee any particular outcome or establish how the Office will resolve an individual SNQ determination.

How Does Estoppel Differ Between Ex Parte Reexamination and IPR?

Estoppel is among the most important strategic differences between the procedures because it can restrict later invalidity arguments.

What estoppel applies to IPR petitioners?

Under 35 U.S.C. 315(e), a petitioner in an IPR that results in a final written decision under Section 318(a) faces statutory estoppel.

The petitioner, its real parties in interest, and privies are restricted from later asserting that a challenged claim is invalid on grounds raised or reasonably capable of being raised during the IPR.

The restriction applies in specified USPTO proceedings and in civil actions or International Trade Commission proceedings.

IPR estoppel does not automatically eliminate every possible invalidity defense. Its application depends on the statute and the particular procedural record.

Nevertheless, petitioners should evaluate available prior art and potential future defenses before filing.

Does ex parte reexamination create equivalent estoppel?

No. Ex parte reexamination has no statutory estoppel provision equivalent to Section 315(e).

That distinction may make the procedure attractive when a challenger wants to preserve flexibility for later disputes.

However, the absence of equivalent statutory estoppel does not mean every argument necessarily remains available.

Other preclusion principles or procedural restrictions may apply. Counsel should confirm their scope in the specific case before relying on reexamination to preserve future defenses.

The practical decision is whether the benefits of active PTAB participation justify IPR’s potential estoppel consequences.

Can Ex Parte Reexamination or IPR Be Discretionarily Denied?

Both procedures can encounter discretionary obstacles even when a challenger presents qualifying prior art.

For IPR, institution requires satisfaction of the statutory threshold and consideration of applicable discretionary factors.

Under Section 325(d), the USPTO may decline institution where substantially the same prior art or arguments were previously presented. Other applicable institution considerations may involve related proceedings and current USPTO policies.

The same statutory provision can affect an ex parte reexamination request.

This is important when evaluating ex parte reexamination discretionary denial as part of a broader challenge strategy.

Switching from IPR to reexamination does not automatically eliminate concerns involving previously considered prior art.

A requester should investigate whether the proposed references or arguments were addressed during original prosecution, earlier reexamination, or other relevant proceedings.

The 2026 pre-order paper procedure provides patent owners an opportunity to address the SNQ determination. It does not replace the separate Section 325(d) analysis.

For both procedures, challengers should assess discretionary issues before investing in extensive filing preparation.

Why Are More Challengers Considering Ex Parte Reexamination in 2026?

Recent filing trends have increased attention on ex parte reexamination as an alternative to IPR.

According to Unified Patents’ Q1 2026 Patent Dispute Report, ex parte reexamination requests were up 157.1% year over year and IPR petitions were down 66.3%, with reexamination requests outpacing new PTAB petitions for two straight quarters.

These figures describe reported filing activity, not the likelihood of success in any particular proceeding.

They also do not establish that reexamination is inherently more effective than IPR.

A challenger should still examine the available evidence, applicable procedural restrictions, participation requirements, and potential estoppel consequences.

For PTAB outcome statistics, see the separate analysis of IPR institution and invalidation rates.

Filing trends provide useful context, but the characteristics of the individual patent dispute should determine the preferred procedure.

When Should a Challenger Choose Ex Parte Reexamination Instead of IPR?

There is no universally preferable procedure.

Ex parte reexamination may be worth considering when qualifying patent or printed-publication prior art supports an SNQ, the challenger does not require extensive participation, and avoiding IPR’s statutory estoppel framework is an important objective.

IPR may be more appropriate when active participation, expert evidence, and an adversarial PTAB process are central to the strategy.

Before selecting either route, counsel should answer several questions.

What is the strongest available prior art? The references must support the applicable procedural standard and claim-specific arguments.

Has the USPTO considered the evidence before? Prior prosecution and administrative proceedings may create Section 325(d) concerns.

Is litigation already pending? Relevant service dates, court deadlines, and available defenses may affect the decision.

How much participation does the challenger need? IPR provides greater opportunities to develop and contest evidence after institution.

What defenses must remain available? Potential estoppel and other preclusion principles should be evaluated before filing.

What is the realistic total budget? Consider legal preparation, expert work, subsequent proceedings, and litigation coordination.

What if neither procedure fits?

Some disputes require a different administrative or judicial route.

For eligible patents, post-grant review may permit a broader range of patentability grounds, subject to its own filing requirements and statutory window.

The inter partes review vs. post-grant review comparison explains these distinctions.

The important point is to match the legal challenge to a procedure that permits the intended arguments.

How Should Patent Owners Respond to Reexamination or IPR?

Patent owners should begin by identifying the exact procedure, challenged claims, asserted prior art, and applicable response deadlines.

For ex parte reexamination, the initial review should determine whether the request qualifies for the April 2026 pre-order paper procedure.

If it does, counsel should promptly assess whether a focused submission addressing the SNQ determination is appropriate.

If reexamination is ordered, the patent owner may respond to Office actions and pursue permitted claim amendments.

For IPR, the patent owner should analyze the petition’s legal grounds, procedural requirements, supporting evidence, and potential arguments against institution.

A preliminary response may address deficiencies in the petition before an institution decision.

If IPR is instituted, the defense may involve expert declarations, briefing, discovery, and other PTAB procedures.

The guide to surviving an IPR petition provides additional context for preparing a defense.

Patent owners should also consider how proposed claim amendments, representations to the USPTO, and related litigation positions may interact.

The immediate priority is a reliable procedural calendar and a focused assessment of the challenge actually presented.

Is Supplemental Examination the Same as Ex Parte Reexamination?

No. Supplemental examination and ex parte reexamination serve different purposes.

Under 35 U.S.C. 257, supplemental examination allows a patent owner to request USPTO consideration, reconsideration, or correction of information believed relevant to an issued patent.

Unlike third-party reexamination requests, supplemental examination is initiated by the patent owner.

It can also involve a broader range of information than the patents and printed publications used for ordinary ex parte reexamination requests.

If supplemental examination identifies a substantial new question of patentability, the USPTO orders reexamination under the applicable statutory framework.

When comparing supplemental examination vs ex parte reexamination, the main considerations are who is requesting review, what information needs examination, and the purpose of the proceeding.

Supplemental examination is not a substitute for a third-party challenger seeking to invalidate a competitor’s patent.

Conclusion

The choice between ex parte reexamination and IPR depends on the available prior art, procedural eligibility, budget, desired participation, and potential litigation consequences.

Ex parte reexamination offers lower listed USPTO request fees, an examination-based process, and no statutory estoppel equivalent to Section 315(e). IPR provides an adversarial PTAB proceeding with defined statutory milestones and significant potential estoppel consequences.

The April 2026 pre-order paper also creates an important early response opportunity for patent owners facing qualifying reexamination requests.

The appropriate procedure is not necessarily the least expensive or most frequently used. It is the one that best supports the specific patentability challenge and broader legal strategy.

FAQs