What is the ex parte reexamination after IPR strategy and when should you use it?

The Ex Parte Reexamination After IPR Strategy: A Definitive Guide for 2026

The ex parte reexamination after IPR strategy is a deliberate, sequential use of two distinct USPTO proceedings: first, an inter partes review (IPR) to challenge patent validity, and second, an ex parte reexamination to address claims that survive or were not included in the IPR. This approach is not a fallback for a failed IPR; rather, it is a calculated, often aggressive tactic that leverages the different procedural rules, claim scope, and estoppel effects of each proceeding. As of August 2026, the USPTO has signaled increased scrutiny of serial challenges, and the Patent Trial and Appeal Board (PTAB) has issued precedential decisions that directly impact how this strategy is executed. Understanding the precise mechanics, timing, and risks is essential for any patent challenger or patent owner facing such a two-front war.

Also worth reading: What is the ex parte reexamination cost breakdown for 2026, and how does the new USPTO pre-order procedure affect total fees? · Ex parte reexamination vs IPR estoppel: Which post-grant challenge avoids estoppel and is the better strategic choice in 2026? · What is PTAB estoppel after an IPR decision and how does it affect patent litigation and reexamination?

The core rationale for pursuing ex parte reexamination after an IPR is to target claims that the IPR did not address—either because the IPR petition was denied as to certain claims, the PTAB did not institute on all challenged claims, or the patent owner amended claims during the IPR to avoid the prior art. Ex parte reexamination allows the challenger (who becomes a third-party requester) to submit prior art and arguments, and the examiner then reconsiders the patent's validity under a broadest reasonable interpretation (BRI) standard, which is generally more favorable to finding invalidity than the Phillips standard used in district court. However, the strategy is fraught with procedural traps, including the § 325(d) discretion to deny reexamination based on prior art already presented to the Office, and the estoppel provisions of 35 U.S.C. § 315(e) that can bar later challenges. This guide provides a comprehensive, practical analysis of when and how to deploy this strategy, based on the latest PTAB and Federal Circuit decisions through early 2026.

Understanding the Interplay: IPR and Ex Parte Reexamination

Inter partes review (IPR) is a trial-like proceeding before the PTAB that allows a petitioner to challenge patent claims on grounds of novelty and obviousness based on prior art patents and printed publications. IPR has a high threshold for institution: the petitioner must demonstrate a reasonable likelihood that at least one challenged claim is unpatentable. Once instituted, the proceeding is conducted under the Phillips claim construction standard, and the petitioner bears the burden of proving unpatentability by a preponderance of the evidence. The IPR process is designed to be a complete resolution of the challenged claims, and it carries a strict estoppel provision under 35 U.S.C. § 315(e): if the IPR results in a final written decision, the petitioner is estopped from asserting in a district court or before the ITC that the claim is invalid on any ground that it raised or reasonably could have raised during the IPR.

Ex parte reexamination, on the other hand, is an older, less adversarial proceeding where the patent owner and the third-party requester have limited participation. The third-party requester files a request with prior art and explanations of substantial new questions of patentability (SNQ). If the Director finds that the request raises an SNQ, the examiner reexamines the patent under the BRI standard, which is more likely to find claims invalid than the Phillips standard. The patent owner can respond with arguments and amendments, but the third-party requester has no right to reply to the patent owner's responses. The proceeding is conducted ex parte, meaning the requester is not a party after the request is granted. This asymmetry can be advantageous to the challenger because the examiner is not bound by the IPR's claim construction or the record, and the reexamination can be used to introduce prior art that was not part of the IPR, such as prior art that was not a patent or printed publication (e.g., public uses or sales) if it can be presented as a printed publication.

The strategic interplay between IPR and ex parte reexamination is not new, but recent PTAB decisions have clarified that the USPTO will not automatically grant reexamination requests that merely rehash arguments already made in a prior IPR. In particular, the PTAB's application of 35 U.S.C. § 325(d) has become a critical gatekeeper. Section 325(d) allows the Director to deny a petition for reexamination if the same or substantially the same prior art or arguments were previously presented to the Office. The Federal Circuit and the PTAB have interpreted this provision broadly, as highlighted in the Mintz article "Reexams Are an Alternative, Not a Fallback: Presentation, Without Consideration, Still Counts Under 35 U.S.C. § 325(d)." This means that even if the prior art was not considered by the examiner in the original prosecution or in the IPR, if it was presented in any form—such as in an information disclosure statement (IDS) or in a petition—the Office may deny reexamination. Therefore, the ex parte reexamination after IPR strategy must be carefully planned to present new prior art that was not previously presented, or to argue that the prior art raises a different SNQ.

When to Use Ex Parte Reexamination After IPR: Strategic Scenarios

The decision to file an ex parte reexamination after an IPR should be based on a clear-eyed assessment of the IPR outcome and the remaining validity risks. There are several scenarios where this strategy is particularly effective.

First, if the IPR petition was denied as to some claims, or the PTAB instituted on only a subset of the challenged claims, the non-instituted claims remain untouched. The petitioner can file an ex parte reexamination to challenge those claims with the same or different prior art. This is especially useful when the IPR was denied due to a discretionary denial under § 314(a) (e.g., because of a parallel district court case), but the prior art is strong. However, the petitioner must be mindful that the § 325(d) discretion may still apply if the prior art was previously presented in the IPR petition, even if the PTAB did not consider it on the merits. As the Crowell & Moring article notes, "Presentation, without consideration, still counts under § 325(d)." Therefore, the reexamination request should emphasize new prior art or a new combination that was not in the IPR petition.

Second, if the IPR resulted in a final written decision where some claims were found patentable, the petitioner is estopped from challenging those claims in district court on grounds that were raised or reasonably could have been raised. However, ex parte reexamination is not subject to the same estoppel because the third-party requester is not a party to the reexamination. The USPTO can reexamine the patent on its own initiative, and the requester can submit prior art that was not raised in the IPR. This allows a second bite at the apple, but only if the prior art is new and raises a different SNQ. The IPWatchdog article "The Reexamination End-Run: When Second Bites at the Apple Become Strategy" highlights that this tactic is increasingly used by defendants who lose an IPR but have additional prior art in their back pocket.

Third, if the patent owner amended claims during the IPR to overcome the prior art, the amended claims are not subject to the IPR's estoppel because they were not finally decided. The petitioner can file an ex parte reexamination to challenge the amended claims with the same prior art that was used in the IPR, but the examiner will apply the BRI standard, which may be more favorable. However, the patent owner will have the opportunity to amend again during reexamination, so the challenger must be prepared for a potentially endless loop of amendments.

Finally, ex parte reexamination can be used as a preemptive strike before filing an IPR, but the question at hand is specifically about using it after an IPR. In that context, the strategy is most effective when the IPR has narrowed the issues, and the challenger has identified specific claims that are vulnerable under a broader claim construction. The key is to avoid duplicative arguments and to present a fresh, compelling SNQ.

The § 325(d) Hurdle: How to Overcome Discretionary Denial

The most significant obstacle to a successful ex parte reexamination after an IPR is the USPTO's discretion to deny the request under 35 U.S.C. § 325(d). This provision states that the Director may reject a petition for reexamination if the same or substantially the same prior art or arguments were previously presented to the Office. The PTAB and the Federal Circuit have interpreted this provision expansively, as evidenced by the HID Global Corporation case, which was remanded by the Federal Circuit for further consideration of § 325(d). In that case, the PTAB had denied a reexamination request because the prior art was presented in a prior IPR, even though the IPR was denied institution. The Federal Circuit held that the PTAB must consider whether the prior art was "previously presented" and whether the arguments were "substantially the same," and that a mere presentation in an IPR petition may be enough to trigger § 325(d) discretion.

To overcome this hurdle, the reexamination request must clearly distinguish the prior art and arguments from those presented in the IPR. This can be done by:

• Identifying prior art that was not cited in the IPR petition or any IDS.
• Presenting a new combination of prior art references that was not previously asserted.
• Arguing that the prior art raises a different SNQ, such as a new claim interpretation or a different statutory ground (e.g., obviousness over a combination that includes a non-patent reference).
• Emphasizing that the IPR was denied institution, and therefore the prior art was never substantively considered by the Office.

However, as the Mintz article warns, "presentation, without consideration, still counts." This means that even if the PTAB never considered the prior art on the merits, if it was presented in the IPR petition, the Office may still deny reexamination. Therefore, the challenger must be prepared to argue that the prior art was not "substantially the same" because the IPR petition did not present it in the context of the specific claims or with the same arguments. In practice, this is a high bar, and many reexamination requests filed after an IPR are denied on § 325(d) grounds. The USPTO has also invited patent owner input to stem the tide of reexamination proceedings, as noted in the Foley & Lardner article, indicating that the Office is aware of the potential for abuse and is tightening its review.

Practical Steps for Filing an Ex Parte Reexamination After an IPR

If you decide to pursue an ex parte reexamination after an IPR, the following steps are essential to maximize your chances of success.

First, conduct a thorough analysis of the IPR record and the patent's prosecution history. Identify the claims that were not challenged or were found patentable, and determine whether any new prior art is available. The prior art must be a patent or printed publication, and it must raise a substantial new question of patentability. The SNQ threshold is lower than the IPR's reasonable likelihood standard, but it still requires a showing that the prior art is more relevant than what was considered during original prosecution.

Second, prepare the reexamination request in accordance with 37 C.F.R. § 1.510. The request must include a statement identifying the SNQ, a detailed explanation of how the prior art applies to the claims, and a copy of the prior art. The request must also include a fee, which is currently $12,600 for a request that includes more than 10 claims, but the fee is reduced for requests with fewer claims. As of 2026, the USPTO has proposed fee increases, so check the current fee schedule.

Third, file the request with the USPTO Central Reexamination Unit (CRU). The CRU will review the request to determine if it raises an SNQ. If granted, the reexamination will proceed, and the patent owner will have two months to file a response. The third-party requester has no right to reply, but can file a paper within two months of the patent owner's response if the patent owner files a response, but only to comment on issues raised by the patent owner's response.

Fourth, monitor the reexamination closely. The examiner will issue an office action, and the patent owner may amend claims. The third-party requester can file comments on the office action, but cannot appeal an adverse decision. If the examiner confirms patentability, the third-party requester has no right to appeal. Therefore, the strategy is best used when the prior art is strong and the claims are clearly invalid under the BRI standard.

Finally, consider the timing. Ex parte reexamination can take an average of 25.3 months to complete, according to USPTO statistics. This is longer than an IPR, which typically concludes within 18 months. If you are in litigation, the reexamination may be stayed, but the district court may not stay the case if the reexamination is filed after the IPR. The IPWatchdog article on the HID remand notes that the timing of the reexamination request relative to the IPR can affect the court's decision to stay.

Comparison: Ex Parte Reexamination vs. IPR vs. PGR

To fully understand the ex parte reexamination after IPR strategy, it is helpful to compare the three main post-grant proceedings: ex parte reexamination, inter partes review, and post-grant review (PGR). The following table summarizes the key differences:

As the table shows, ex parte reexamination is the only proceeding that does not impose estoppel on the requester, which is a significant advantage. However, the lack of participation and appeal rights makes it a less attractive option for complex challenges. The IPR is the most popular because it offers a trial-like process and estoppel benefits for the petitioner, but the estoppel can be a double-edged sword if the petitioner loses. PGR is limited to certain grounds and must be filed within 9 months of grant, making it less useful for older patents.

Common Mistakes and Pitfalls to Avoid

Several common mistakes can derail an ex parte reexamination after IPR strategy. The most frequent is filing a reexamination request that relies on the same prior art and arguments as the IPR, which will almost certainly be denied under § 325(d). To avoid this, conduct a fresh prior art search and focus on references that were not cited in the IPR. Another mistake is underestimating the patent owner's ability to amend claims during reexamination. The patent owner can narrow the claims to overcome the prior art, and the third-party requester has no opportunity to challenge the amended claims. Therefore, the request should anticipate potential amendments and include arguments that would apply to foreseeable amendments.

A third mistake is ignoring the estoppel implications of the IPR. Even though ex parte reexamination does not have estoppel, the IPR's estoppel can affect the reexamination if the same grounds are raised. The examiner may consider the IPR's final written decision and give it deference, especially if the claims are identical. Therefore, the reexamination request should emphasize that the prior art raises a different SNQ than the IPR grounds.

A fourth mistake is filing the reexamination request too late. If the patent is in litigation, the district court may have already issued a claim construction order, and the reexamination may be stayed or denied. The USPTO has also been more willing to deny reexamination requests that are filed solely to delay litigation. The Proskauer Rose article on PTAB strategic recalibration notes that courts are increasingly skeptical of serial challenges and may impose sanctions for abuse.

Finally, a fifth mistake is failing to consider the cost-benefit analysis. Ex parte reexamination can be expensive, and the third-party requester has no guarantee of success. The USPTO has invited patent owner input to stem the tide of reexamination proceedings, indicating that the Office is aware of the potential for abuse and is tightening its review. Therefore, only pursue this strategy if you have strong, new prior art and a clear path to invalidating the claims.

When to Act: Timing and Strategic Considerations

The timing of an ex parte reexamination after an IPR is critical. The best time to file is immediately after the IPR final written decision, but before the district court trial or the ITC hearing. This allows the reexamination to proceed in parallel with litigation, and the court may stay the case pending the reexamination outcome. However, the court is not required to stay, and the reexamination may not conclude before the trial date. As of 2026, the average time to completion for ex parte reexamination is 25.3 months, which is longer than the 18-month IPR timeline. Therefore, if the trial is scheduled within 12 months, the reexamination may not be useful.

Another timing consideration is the patent's expiration date. Ex parte reexamination can be filed even after the patent expires, as long as the patent is still enforceable. However, the reexamination will not affect expired claims, and the patent owner may not have a strong incentive to respond. In that case, the reexamination may be a waste of resources.

Finally, consider the impact of the USPTO's recent policy changes. The PTAB has become more willing to deny IPR petitions under § 314(a) and § 325(d), and the same scrutiny applies to reexamination requests. The Crowell & Moring article on strategic considerations in light of recent PTAB policy changes advises that challengers should be prepared to argue why the reexamination is not duplicative and why the prior art was not previously considered. The USPTO has also proposed rules to limit the number of reexamination requests that can be filed on the same patent, so check the latest rules.

Cost and Resource Allocation

The cost of an ex parte reexamination after an IPR can be substantial. The USPTO fee for a reexamination request is $12,600 for a large entity, but this is just the filing fee. Attorney fees for preparing the request can range from $20,000 to $50,000, depending on the complexity of the prior art and the number of claims. The patent owner's response and the examiner's office actions will require additional monitoring, which can add another $10,000 to $20,000. In total, a reexamination can cost between $50,000 and $100,000, which is comparable to the cost of an IPR, but with less control over the outcome.

Given the high cost and the risk of denial under § 325(d), it is essential to conduct a cost-benefit analysis. If the patent is a blocking patent that threatens your product, the cost may be justified. However, if the patent is of marginal relevance, it may be better to focus on other defenses, such as non-infringement or invalidity in district court. The AI Patent Review tool can help you assess the strength of the prior art and the likelihood of success, but it cannot replace a thorough legal analysis.

Conclusion: Is the Ex Parte Reexamination After IPR Strategy Right for You?

The ex parte reexamination after IPR strategy is a powerful but risky tool. It is not a fallback for a failed IPR; rather, it is a deliberate, second-line attack that can be used to challenge claims that survived an IPR or were not included. The key to success is to present new prior art that raises a substantial new question of patentability, and to avoid the § 325(d) trap by distinguishing the prior art and arguments from those previously presented. The strategy is best used when the IPR has narrowed the issues, and the challenger has a strong, new prior art reference that was not previously considered. However, the lack of participation and appeal rights, the long timeline, and the high cost make it unsuitable for every case. As of August 2026, the USPTO is scrutinizing reexamination requests more closely, and patent owners are actively opposing them. Therefore, before filing, consult with experienced counsel and consider using AI tools to analyze the prior art and predict the outcome. With careful planning, the ex parte reexamination after IPR strategy can be an effective way to invalidate a patent that would otherwise block your business.

FAQ

Can I file an ex parte reexamination after an IPR if the IPR was denied institution?

Yes, you can file an ex parte reexamination after an IPR denial, but the USPTO may deny the reexamination under 35 U.S.C. § 325(d) if the prior art was presented in the IPR petition, even if the PTAB never considered it. To overcome this, you must present new prior art or argue that the prior art raises a different substantial new question of patentability. Does the estoppel from an IPR apply to ex parte reexamination?

No, the estoppel under 35 U.S.C. § 315(e) applies only to the petitioner in the IPR and prevents them from asserting invalidity in a district court or ITC on grounds that were raised or reasonably could have been raised. Ex parte reexamination is a separate proceeding, and the third-party requester is not estopped from submitting prior art, but the examiner may consider the IPR's final decision. How long does an ex parte reexamination take after an IPR?

As of 2026, the average time to completion for an ex parte reexamination is approximately 25.3 months, which is longer than an IPR's 18-month timeline. The actual duration can vary depending on the complexity of the case and the number of claims. What is the cost of filing an ex parte reexamination after an IPR?

The USPTO filing fee for a reexamination request is $12,600 for a large entity, but attorney fees can add $20,000 to $50,000 or more. The total cost, including monitoring and responses, can range from $50,000 to $100,000. Can a patent owner amend claims during ex parte reexamination?

Yes, the patent owner has the right to amend claims during ex parte reexamination to overcome the prior art. The third-party requester has no right to challenge the amended claims, so the request should anticipate potential amendments and include arguments that would apply to foreseeable amendments.

Quick Facts

• Category: Post-Grant Proceedings
• Timeline: 25.3 months average for ex parte reexamination; IPR takes ~18 months
• Cost: $12,600 USPTO fee plus $20,000-$50,000 in attorney fees; total $50,000-$100,000
• Best for: Challengers with new prior art not previously presented to the USPTO

Sources

• https://www.mintz.com/insights-center/viewpoints/2026-01-reexams-are-alternative-not-fallback
• https://www.crowell.com/en/insights/client-alerts/ex-parte-reexamination-strategic-considerations-for-patent-challengers
• https://ipwatchdog.com/2026/02/15/what-the-usptos-reexamination-remand-for-hid-means-for-estoppel-timing-and-strategy/
• https://www.jdsupra.com/legalnews/can-a-discretionary-ipr-denial-also-shut-2976543/
• https://ipwatchdog.com/2026/03/01/the-reexamination-end-run-when-second-bites-at-the-apple-become-strategy/
• https://www.proskauer.com/insights/back-to-district-court-ptab-strategic-recalibration-in-patent-litigation
• https://www.foley.com/en/insights/publications/2026/04/uspto-invites-patent-owner-input-to-stem-tide-of-reexamination-proceedings

Follow-Up Keyword

ex parte reexamination vs IPR estoppel