IPR vs. Ex Parte Reexamination: How the Two Patent Challenges Differ

Sources: 35 U.S.C. §§ 302-307, § 311, § 312, § 314, § 315, § 316; 37 C.F.R. § 1.20(c), § 1.510, § 1.530(j), § 42.15, § 42.100, § 42.102; MPEP chapter 2200; USPTO Central Reexamination Unit; Consumer Watchdog v. WARF (Fed. Cir. 2014); USPTO ex parte reexamination filing data (Sept. 30, 2025). Each row is explained below.

"Any person at any time may file a request for reexamination" (35 U.S.C. § 302); the rule says any time "during the period of enforceability of a patent" (37 C.F.R. § 1.510(a)). That includes the patent owner, licensees, accused infringers and companies with no dispute yet. There is no one-year bar after a lawsuit, so reexamination remains open after the IPR deadline has passed. The only bar is IPR and PGR estoppel: after a final written decision on a claim, the petitioner, its real party in interest and privies may not request reexamination of that claim on a ground they raised or reasonably could have raised in the review (§§ 315(e)(1), 325(e)(1); § 1.510(a); MPEP § 2212). A third-party requester must certify that this estoppel does not apply (§ 1.510(b)(6)).

An IPR petition may be filed only by someone "who is not the owner of a patent" (§ 311(a)), only after the date nine months after grant for a first-inventor-to-file patent, or after grant for an older one, and not during an instituted PGR (§ 311(c); 37 C.F.R. § 42.102). It is barred if the petitioner or its real party in interest first filed a civil action challenging validity; an invalidity counterclaim does not count (§ 315(a)). And it may not be instituted if filed more than one year after the petitioner, its real party in interest or privy was served with an infringement complaint, though that limit does not apply to a request for joinder (§ 315(b)).

Anonymity. An IPR petition "may be considered only if" it "identifies all real parties in interest" (§ 312(a)(2)). Reexamination does not require that today: a real party in interest may stay anonymous by having a registered practitioner file the request (MPEP § 2212). Two recent changes narrow that:

• Previously challenged patents (notice dated Feb. 4, 2026, 1544 OG 128). Where any claim of the patent has received a final written decision in an IPR or PGR, an anonymous request should include an affirmative statement that the real party in interest is not that proceeding’s petitioner or its real party in interest or privy, and identify the earlier proceedings and parties. Without it, the request’s filing date may be vacated.
• Proposed rule (July 22, 2026). The USPTO proposed requiring every third-party requester to identify all real parties in interest (RIN 0651-AD94). Comments closed August 21, 2026; no final rule had been published as of October 15, 2026.

Sources: 35 U.S.C. § 302, § 311, § 312(a)(2), § 315(a)-(b); § 325(e); 37 C.F.R. § 1.510, § 42.102; MPEP § 2212; Filing Anonymous Requests for Ex Parte Reexamination Directed to Previously-Challenged Patents, 1544 OG 128 (Mar. 3, 2026); Requirement To Identify All Real Parties in Interest, 91 FR 46038 (proposed July 22, 2026).

Reexamination is ordered when the request raises "a substantial new question of patentability affecting any claim" (§ 303(a)), decided within three months of filing. Under the MPEP, a question is substantial when "a reasonable examiner would consider the teaching to be important in deciding whether or not the claim is patentable," and new when the same question as to that claim has not already been decided in an earlier concluded Office examination or review, raised in a pending reexamination or supplemental examination, or decided in a final federal-court holding of invalidity on the merits after all appeals. It does not require a prima facie case of unpatentability. Art the examiner already saw can qualify: by statute the question is "not precluded by the fact that a patent or printed publication was previously cited by or to the Office or considered by the Office" (§ 303(a)), though the MPEP still requires a new, non-cumulative teaching or a new light on old art.

Historically the bar has been low in practice: of 15,998 decisions on requests through September 30, 2025, 92.7% granted reexamination. Requests have also risen sharply: 491 in fiscal year 2025, and 831 in the first three quarters of fiscal year 2026 (through June 30, 2026).

IPR requires "a reasonable likelihood that the petitioner would prevail with respect to at least 1 of the claims challenged" (§ 314(a)), and since October 20, 2025 the Director decides IPR institution (and may refer a decision to PTAB judges), weighing the merits together with discretionary considerations such as parallel litigation, earlier challenges and how long the claims have been in force. Both proceedings are subject to 35 U.S.C. § 325(d), which lets the Director reject a request or petition that presents "the same or substantially the same prior art or arguments" the Office has already seen; in reexamination that question is taken up after the substantial-new-question determination.

Sources: 35 U.S.C. § 303, § 314, § 325(d); 37 C.F.R. § 1.515; MPEP §§ 2216, 2242; ex parte reexamination filing data (Sept. 30, 2025); reexamination operational statistics (quarter ending June 30, 2026); Pre-order Procedure regarding Substantial New Question determination, 1545 OG 217 (Apr. 28, 2026); Director Institution of AIA Trial Proceedings (Oct. 17, 2025).

Ex parte reexamination.

1. The request must state each substantial new question, explain how the cited art applies to every claim for which reexamination is requested, and include copies of the art and the patent (37 C.F.R. § 1.510(b)). It is served on the patent owner.
2. New in 2026: for requests filed on or after April 5, 2026, the patent owner may file a "pre-order paper" of up to 30 pages, within 30 days after service of the request, arguing that despite the teachings the request cites the Office should keep its earlier decision of patentability. The paper may not dispute that a teaching is new, raise matters outside the request, or argue for denial under § 325(d). A requester may respond only in exceptional cases, with a grantable petition and fee, in 10 pages within 15 calendar days after service of the patent owner’s paper. Neither period can be extended. Before this, § 1.530(a) barred a patent owner statement before the order, except with a request the owner filed itself.
3. If reexamination is ordered, the patent owner has at least two months to file a statement, with any amendments or new claims, and the requester may reply within two months of service, but only if the patent owner files a statement (§ 304; §§ 1.530, 1.535).
4. Examination then proceeds ex parte, "according to the procedures established for initial examination," with "special dispatch" (§ 305). The requester does not take part.
5. The patent owner may appeal adverse decisions to the PTAB and the Federal Circuit (§ 306). The proceeding ends with a certificate cancelling, confirming or adding claims (§ 307).

Inter partes review. The patent owner may file a preliminary response within three months of the notice according the petition a filing date and, under the Director’s interim process, a separate brief requesting discretionary denial within two months of that notice; institution is decided within three months after the preliminary response, or after its due date if none is filed (§ 314(b)). An instituted trial runs on a scheduling order: patent owner response and any motion to amend, petitioner reply, sur-reply, depositions of each side’s declarants, and an oral hearing, with a final written decision due one year after institution, extendable by up to six months for good cause and adjustable for joinder (§ 316(a)(11)). The petitioner must prove unpatentability by a preponderance of the evidence (§ 316(e)). Either party may appeal (§ 319), if it has Article III standing.

Claim construction differs. A reexamination examiner gives unexpired claims "the broadest reasonable interpretation consistent with the specification" and uses the court standard only for an expired patent (MPEP § 2258). In IPR, claims are construed under the same standard used in a civil action (37 C.F.R. § 42.100(b)). A broader reading in reexamination can capture more prior art.

Sources: 35 U.S.C. §§ 304, 305, 306, 307, 314, 316, 319; 37 C.F.R. §§ 1.510, 1.530, 1.535, 1.550, 42.100, 42.107; MPEP §§ 2209, 2258; 1545 OG 217 (Apr. 28, 2026); Interim Processes for PTAB Workload Management (Mar. 26, 2025); PTAB Consolidated Trial Practice Guide (Dec. 2025).

In reexamination the patent owner "will be permitted to propose any amendment to his patent and a new claim or claims thereto," so long as no claim is enlarged in scope (§ 305) and no new matter is added; no amendment may be proposed in an expired patent (37 C.F.R. § 1.530(j)). The patent owner has at least 30 days to answer each Office action (37 C.F.R. § 1.550(b)). The USPTO’s data show what that means: in the USPTO’s analysis of certificates issued through September 30, 2025, 22.2% confirmed all requested claims, 14.5% cancelled all requested claims and 63.3% changed claims. For third-party requests the figures were 22.9%, 16.1% and 61.0%. (The analysis covers requested claims only and counts merged reexaminations once.)

In IPR the patent owner may file one motion to amend, to cancel claims or propose "a reasonable number of substitute claims," which may not enlarge scope or add new matter (§ 316(d)). Either way, amended or new claims that come out of the proceeding have the same effect as reissued claims under § 252 for anyone who, before the certificate, made, purchased or used within the United States, or imported into the United States, what the new claims cover, or made substantial preparation to (§§ 307(b), 318(c)).

Sources: 35 U.S.C. § 305, § 307, § 316(d), § 318; 37 C.F.R. § 1.530(j), § 1.550; ex parte reexamination filing data (Sept. 30, 2025).

If the USPTO refuses to order reexamination, the request fee is refunded except for a refused-request fee of $3,780 for a large entity ($1,512 small, $756 micro).

These are government fees; attorney and expert costs come on top, and an IPR adds adversarial discovery, including depositions of the other side’s declarants, and a right to an oral hearing (§ 316(a)(5), (10)); reexamination considers declarations too, but without that discovery (MPEP § 2216). Our official sources do not quantify those costs.

Sources: 37 C.F.R. § 1.20(c), § 1.26(c), § 42.15, § 42.107(b); USPTO fee schedule; 35 U.S.C. § 303(a), § 314(b), § 316(a)(5), (10), (11); MPEP § 2216; ex parte reexamination filing data (Sept. 30, 2025).

• IPR estoppel. After a final written decision, the petitioner, its real party in interest and privies may not request or maintain a USPTO proceeding on that claim, or argue invalidity in court or at the ITC, on any ground raised or that "reasonably could have" been raised (§ 315(e)). The Federal Circuit applies estoppel "not just to claims and grounds asserted in the petition and instituted for consideration by the Board, but to all claims and grounds not in the IPR but which reasonably could have been included in the petition" (Caltech v. Broadcom, 2022). So after a final written decision, the petitioner cannot use reexamination to retry that claim on grounds it raised or reasonably could have raised in the IPR.
• No estoppel from reexamination. Chapter 30 of the Patent Act (§§ 302-307) contains no estoppel against the requester, so a reexamination requester may still raise the same art in court. But the requester has no right to appeal a confirmation (§ 306 gives that right to the patent owner), and its say ends with the reply after the order.
• Reexamination can strengthen the patent. Claims confirmed or amended over your art come out with a certificate (§ 307). In court, a challenger may point out that the USPTO never had its best art before it, because then the Office’s "considered judgment may lose significant force" (Microsoft v. i4i, 2011); once the art has been through reexamination, that point is gone. Request reexamination only on art you are prepared to see the examiner consider and the patent owner amend around.
• Overlapping proceedings. While an IPR is pending, the Director may stay, transfer, consolidate or terminate another USPTO proceeding on the same patent (§ 315(d)), and if the patent is in litigation the Director decides whether to suspend a reexamination (37 C.F.R. § 1.565(b)).
• A pending IPR rule. A rule proposed on October 17, 2025 (RIN 0651-AD89) would, among other things, generally bar IPR on a claim "found patentable" in an ex parte reexamination requested by someone other than the patent owner or its real party in interest or privy, unless the Director personally institutes in extraordinary circumstances. It was not final as of October 15, 2026.

Sources: 35 U.S.C. § 315(d)-(e), §§ 302-307; 37 C.F.R. § 1.565; MPEP § 2286; California Institute of Technology v. Broadcom Ltd., 25 F.4th 976 (Fed. Cir. 2022); Microsoft Corp. v. i4i Limited Partnership, 564 U.S. 91 (2011); Revision to Rules of Practice Before the PTAB, 90 FR 48335 (proposed Oct. 17, 2025).

• Reexamination fits when you are past the IPR one-year bar, want to stay out of view (through a practitioner, subject to the 2026 notice and the pending proposal), have a strong single reference that maps cleanly onto the claims, or cannot fund a trial. It also suits a patent owner who wants the Office to consider new art and amend before enforcing.
• IPR fits when you need to control the argument through the end, want expert testimony and cross-examination, and can accept estoppel, and when the case can survive the Director’s discretionary review. Check whether the claims were already upheld elsewhere or are being litigated on a faster schedule; those facts now weigh against institution.
• Neither proceeding can raise eligibility, § 112 or prior public uses and sales against original claims; within nine months of grant, a first-inventor-to-file patent can face those (though never best mode) in post-grant review. For invalidity in litigation, see PTAB vs. district court.

Follow how the Board and the Director are ruling on our PTAB hub, with PTAB guidance and memoranda, discretionary denial decisions and institution statistics on the PTAB dashboard.

Sources: 35 U.S.C. § 302, § 311(b), § 315(b), (e); 37 C.F.R. § 1.552; 1544 OG 128 (Mar. 3, 2026); Interim Processes for PTAB Workload Management (Mar. 26, 2025). Which route fits is our own view, not legal advice.