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FDA launches expedited IND pilot, fills in details on its design

The FDA opened its expedited IND pilot program to applications Sept. 15, pushing forward with one of its highest-profile initiatives to explore new ways of accelerating first-in-human research in the U.S. The agency plans to accept applications through Oct. 30 and select between eight and 10 pairs of participating sponsors and research institutions by mid-December.

By Ned Pagliarulo | Sep 15, 2026 9:32 PM EDT

Background on FDA’s clinical trial reform efforts

  • Clinical trial activity is shifting away from the U.S. China now accounts for more of the world’s early-stage drug research than the U.S., while countries such as Australia have attracted sponsors with flexible regulatory schemes that support rapid initiation of first-in-human trials. Over the past year, these trends have roused urgent warnings from U.S. lawmakers, biotech executives and researchers, who have called for reforms to improve the nation’s trial ecosystem and bolster U.S. competitiveness in the life sciences. [Read AgencyIQ’s analysis of how comparisons to China and Australia are shaping proposals for trial reform in the U.S.]
  • Human testing of experimental drugs in the U.S. is regulated through the FDA’s Investigational New Drug application process, outlined in 21 CFR 312. These applications must contain preclinical pharmacology and toxicology data, manufacturing details, clinical protocols, and information for the physicians who will administer the experimental treatment. Upon receipt of an IND, the FDA has 30 calendar days to review the application, after which the sponsor may proceed.
  • In practice, however, the IND process has become both lengthy and costly. Drugmakers spend considerable time assembling the required information, often meeting with the FDA along the way to ensure their application will be complete upon submission. Negotiations with the institutional review boards that oversee experimental patient treatment add further time, often after the FDA has given a green light. This has slowed trial initiations in the U.S. and motivated companies to seek out other locations, such as Australia. Former FDA Commissioner MARTIN MAKARY spoke on the burdens of this process often during his tenure, noting how the length of time between a sponsor’s “pre-IND” meeting with the FDA and its actual application submission was nearly twice as long as the equivalent period in China.
  • On June 22, 2026, the FDA unveiled plans for a new pilot program to speed first-in-human trials. The announcement was made through a request for information, which coincided with rollout of “Operation TrialBlazer,” an HHS-wide initiative to “strengthen America’s leadership in clinical research,” according to an HHS statement. The proposed pilot is a central part of the FDA’s contributions to the project, which also involve new guidance and resources for sponsors. [Read AgencyIQ’s in-depth analysis of Operation TrialBlazer here.]
  • The FDA also aims to support domestic Phase 1 trials through rulemaking and a revised user fee structure. The Unified Agenda published in July lists records for two proposed rules that would amend 21 CFR 312 to revise IND requirements and update the responsibilities the agency outlines for sponsors and investigators. The regulation change is intended to implement expedited IND reforms by providing “targeted, risk-based flexibilities.” [Read AgencyIQ’s full analysis of the Unified Agenda here.] Meanwhile, in negotiations ahead of next year’s Prescription Drug User Fee Act reauthorization, the FDA and industry agreed to a proposal to modify the current user fee structure. A recent Federal Register notice describes a new structure under which sponsors would receive a 50% discount in application fees if their submission includes clinical data from at least one Phase 1 trial “anchored” in the U.S. The intent is to encourage domestic trial initiation. [Read AgencyIQ’s full analysis of the draft commitment letter here.]

Proposed pilot would establish research network, implement rolling IND submissions

  • The FDA envisions that its proposed IND pilot will reduce trial initiation timelines in two principal ways. Through it, the agency would recruit external research institutions to provide advice and preliminary review on IND submissions prepared by trial sponsors – an exchange that the FDA expects could strengthen the resulting applications. Higher-quality submissions would potentially reduce the frequency with which the regulator needs to intervene to halt pending research over safety concerns. Simultaneously, the FDA would explore allowing “rolling” IND submissions that would give it the opportunity to review completed components of the application before the overall package is submitted. The statutory 30-day clock would begin upon receipt of the last component, but, because the agency would have already assessed most of the information, it may be able to give sponsors a green light to proceed with testing before the review period ends. The FDA also noted the potential for other trial initiation activities, such as IRB reviews and site contracting, to take place in parallel with IND development through the pilot. [Read AgencyIQ’s full analysis of the RFI here.]
  • The pilot would be built around a network of “qualified research institutions.” The RFI defines these institutions broadly. They could be academic medical centers, health care networks, contract research organizations or another kind of third-party advisor. Their role is limited only to provide “advice and preliminary review,” however. “FDA will remain solely responsible for making decisions about whether a clinical investigation can begin or whether a clinical hold may be imposed,” the RFI states. Essentially, these QRIs would become expert partners to help trial sponsors develop the pharmacology and toxicology, clinical, and chemistry, manufacturing and controls components of an IND submission.
  • The FDA received extensive feedback on its RFI on the proposed expedited IND pilot program. More than 200 research and industry associations, drug developers, medical societies, patient groups and individuals provided input by the agency’s deadline of Aug. 24, 2026. Industry stakeholders almost universally supported the pilot’s objective, agreeing with the FDA that Phase 1 trials could be accelerated in the U.S. Many also viewed the pilot as a worthwhile experiment to test new approaches. However, some stakeholders raised concerns about whether QRIs would duplicate work that the FDA would ultimately still complete or questioned whether the QRI-sponsor relationship would create new conflicts of interest. Others shared skepticism that introducing a QRI network to the process would meaningfully speed timelines, urging the FDA to focus on reforming its IND processes and requirements more generally. [Read AgencyIQ’s full analysis of industry comments here.]

FDA launches IND pilot

  • The FDA formally debuted its expedited IND pilot on Sept. 15, announcing the program’s final design and opening it to applications from sponsors and QRIs. The agency expects to accept applications through Oct. 30 and select between eight and 10 sponsor-QRI pairs by Dec. 18, although it may adjust the timeline based on the number of submissions received. An associated webpage the FDA also published Sept. 15 lists factors by which it will prioritize and evaluate submissions. The webpage also outlines the rolling submission process and provides application instructions to sponsors and QRIs.
  • The FDA will prioritize submissions involving INDs for novel products overseen by the Center for Drug Evaluation and Research’s Office of New Drugs, the Center for Biologics Evaluation and Research’s Office of Therapeutic Products, or the Oncology Center of Excellence. The agency will also favor INDs classified as commercial and related to a first-in-human study that the sponsor intends to run in the U.S., according to the agency webpage. Sponsors should have “sufficient preliminary nonclinical data” to aid the FDA’s evaluation of proposed timelines for development and IND submission. And while the IND can incorporate a novel drug technology or platform, sponsors should not seek to use the pilot for supporting development of the platform or technology more broadly. When considering prospective QRIs, meanwhile, the FDA will prioritize institutions doing business in the U.S. that commit to providing support across nonclinical, manufacturing and clinical disciplines. It will also prioritize QRIs that can support trial initiation through “owned infrastructure or formally documented partnership agreements.”
  • Sponsors and QRIs are responsible for managing possible conflicts of interest. The FDA wrote on its pilot webpage that it expects QRIs will have in place written procedures that describe processes for identifying, assessing and managing real or potential conflicts. For QRIs that own or operate IRBs, the written procedures should also make sure IRB members don’t also participate in the QRI’s advisory work as part of the pilot. The FDA wrote that it would remove sponsor-QRI pairs from the pilot if it determines that conflicts of interest “compromised a QRI’s ability to provide objective recommendations.”
  • The FDA aims to select a diverse group of IND submissions and QRIs, and will therefore evaluate applications relative to each other. “FDA will seek to ensure the selected cohort reflects breadth across therapeutic areas, product modalities, sponsor sizes, and QRI types,” the program webpage states. When evaluating INDs, the FDA will consider their complexity and fit with rolling submission format. The agency will also weigh whether the IND is at a stage when QRI advice would be meaningful as well as the severity and burden of the condition that the drug is meant to address. As the pilot is meant to test the QRI relationship’s value, the FDA plans to select both small biotechnology companies and larger, more experienced companies.
  • QRIs will be assessed on their “documented experience” across seven disciplines: nonclinical, manufacturing, clinical, pharmacology, regulatory affairs, trial support and “program-specific” expertise, such as experience with novel therapies, rare diseases or “other modalities,” the webpage states. The FDA expects that QRIs will either have “self-owned clinical trial infrastructure or documented partnership arrangements with IRB-approved clinical trial sites sufficient to support site activation activities.” QRIs can contract with external experts or organizations to supplement their own expertise but will remain responsible for making readiness determinations on the sponsor’s IND submission in the pilot.
  • The FDA plans to assess whether the pilot helps to achieve various trial acceleration outcomes. These are described in general, qualitative terms on the program webpage, rather than by any quantitative metric or compared to any historical baseline. Specifically, the FDA hopes the pilot will improve “quality and submission of phase-appropriate data” for first-in-human INDs; identify and resolve issues that may delay trial initiation; reduce Phase 1 clinical holds or information requests; make nonclinical development more efficient; and better coordinate trial startup activities. The agency also plans to collect written and verbal feedback on the “overall process, lessons learned and the specific role the QRI played at each stage,” according to the webpage.
  • The FDA also provided additional details on the rolling submission process. A sponsor will submit discipline-specific IND components on a piecemeal basis after its partner QRI determines whether it “incorporates scientifically sound rationale and data,” the webpage states. Sponsors can determine the sequence by which they submit IND components through the FDA’s Electronic Submissions Gateway. Their submissions should be “discrete, self-contained” packages rather than “partial or fragmentary” data drops. The FDA’s 30-day review clock will begin once sponsors submit their final IND, which can contain components not previously submitted on a rolling basis.

Analysis

  • The FDA incorporated feedback it received on its June RFI into the pilot’s final design, CDER Director MIKE DAVIS said on a press call held prior to the announcement. The overall framework for the pilot remains largely unchanged from the agency’s original proposal, however. For instance, the considerations the FDA plans to weigh when assessing a QRI roughly match the qualification criteria it had outlined in June, despite the considerable input the agency received on this front. The webpage does mention that the FDA will consider whether a prospective QRI can deliver program-specific expertise, which may reflect requests from many stakeholders to permit QRI specialization.
  • The FDA will not require a QRI to operate a self-owned IRB, potentially relieving the many stakeholders who commented that doing so could unnecessarily restrict the pool of potential QRIs. However, the agency does expect institutions to have “documented partnership arrangements” that can support IRB activities in parallel to IND review. This may still favor institutions that support a wide range of trial activities over organizations that can advise specifically on nonclinical or regulatory affairs topics but don’t typically handle trial activation and initiation. That said, an FDA spokesperson said on the agency’s press call that the FDA plans to diversify the type of participating QRIs so the pilot doesn’t only involve academic medical institutions.
  • The FDA defended the pilot against some concerns raised by stakeholders. Several commenters, including industry trade groups BIO and PhRMA, had expressed doubt about the QRI model’s value and wondered whether it would create duplicative work. On the press call, the FDA spokesperson said that, while the agency would assess the pilot carefully, it doesn’t think the QRI model will add additional bureaucracy. “If implemented properly, companies would be able to hopefully have quicker interaction back-and-forth with the QRIs that they’re working with and resolving issues,” the spokesperson said. Many commenters had also raised alarm about the potential for conflicts of interest if QRIs advise on research and operate or arrange the review boards that oversee it. The FDA expects participating institutions will have procedures to prevent this and, in any case, the agency will retain full review authority over submissions and any deficiencies they might contain. “We don’t believe, at least at this point in time, that there are any conflicts of interest that we would be dealing with for this,” the spokesperson said.
  • The pilot’s predominant focus is on testing whether the sponsor-QRI relationship can speed up pre-IND timelines. CBER Director Karim Mikhail previously acknowledged this on a Aug. 6 industry webinar. “We all know that the IND submission itself, the 30 days, yes, there is room to save, but the savings there is very limited,” Mikhail said. “Most of the savings is in the pre-IND phase and in the post-IND phase.” The rolling submission of IND application components happens during this phase as well, allowing sponsors to get feedback first from QRIs and then from the FDA. The hope is that this feedback allows for earlier identification of potential shortcomings, allowing them to be remedied before full IND submission and (potentially) avoiding a clinical hold that could delay testing.
  • How quickly could the pilot provide useful information? Debate over the U.S. response to China’s competitive threat is already in full swing. Industry and the FDA have wrapped their Prescription Drug Use Fee Act negotiations, and Congress will consider the reauthorization bill next year. For the pilot to provide data that helps shape the eventual legislative package – often a vehicle for other FDA-related reforms – the FDA will need to move quickly. The agency’s launch of this pilot so soon after collecting feedback likely reflects this demand. However, several stakeholders suggested the pilot run for at least one year to draw representative conclusions, which could mean that its lessons arrive after user fee reauthorization occurs. The agency did not provide any indication of the pilot’s length in announcing its design Sept. 15 and noted that it doesn’t intend to “enforce strict timelines” on QRI interactions with sponsors.
  • The FDA views the pilot as potentially providing a foundation for larger changes in the future. In its Sept. 15 statement, the agency said it “may inform future policy initiatives,” such as a formal accreditation model for research institutions that demonstrate “strong scientific and regulatory judgment.” Davis and CBER Director KARIM MIKHAIL made similar indications on the press call. “What we learn from this first cohort can help inform the future of early-stage drug development in the United States,” said Mikhail. Currently, the FDA will retain full oversight authority over the INDs prepared and evaluated through the pilot. Yet the FDA’s statement indicates it can foresee a future in which QRIs take on a greater role, perhaps akin to human research ethics committees in Australia, to whom review of certain lower-risk trials is delegated by the country’s regulator. The FDA referenced Australia’s system in its most recent budget request to Congress, which asks lawmakers to create a new “clinical trial notification pathway.”

To contact the author of this item, please email Ned Pagliarulo ( npagliarulo@agencyiq.com).
To contact the editor of this item, please email Jason Wermers ( jwermers@agencyiq.com).

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