The National Institutes of Health (NIH), long viewed as the crown jewel of American biomedical research, is facing unprecedented upheaval as political battles, bureaucratic shakeups, and funding freezes threaten to undermine its core mission. In recent months, a combination of deep budget cuts, controversial new oversight bodies, and high-profile legal wrangling with elite universities has put the future of U.S. science funding in a precarious state.
Historically, the NIH has commanded a budget of nearly $50 billion each year—an amount exceeding the gross domestic product of many small nations. Its bipartisan support has been rooted in the agency’s outsized role in driving breakthroughs for diseases like cancer, heart disease, and Alzheimer’s. However, as reported by STAT News, the landscape shifted dramatically after the COVID-19 pandemic, when the NIH came under fire for a perceived lack of transparency, especially regarding its sponsorship of research in Wuhan, China.
Those criticisms, initially focused on virology, have now snowballed into a broader campaign against the NIH’s structure and spending. The Trump administration, with President Trump and Health and Human Services Secretary Robert F. Kennedy Jr. at the helm, has slashed the NIH’s proposed budget by around 40%. Ongoing grants have been cut or frozen, and more than 1,000 NIH employees have been laid off. According to STAT News, these moves are part of the administration’s “Make America Healthy Again” agenda, which touts efficiency and accountability but has drawn sharp rebuke from many in the research community.
Yet, the changes go beyond mere cost-cutting. The newly established Department of Government Efficiency (DOGE), created by executive order in January 2025, has become a powerful force in federal grant management. As detailed by The Harvard Crimson, DOGE has taken control of the Payment Management System (PMS)—the platform used to track and release federal grants. This new oversight regime, branded “Defend the Spend,” requires both grant issuers and recipients to justify awards before funds are released. If a grant does not align with administration priorities, DOGE can block payment—even if the NIH has already approved the funding.
This system has led to a patchwork of winners and losers among America’s top research universities. In July 2025, following a ruling by District Judge William G. Young, the NIH began allocating some grants to Harvard University in compliance with a federal court order that directed the Trump administration to reinstate more than $2.7 billion in federal grants previously frozen or terminated. However, according to The Crimson, DOGE officials quietly blocked all NIH funds to Harvard at the last mile, withholding money because the university had not reached a settlement with the White House. The only other school to face a total block was Northwestern University, which also had not settled.
Meanwhile, Columbia University and Brown University only saw their NIH funding restored after striking multi-million dollar deals with the White House in late July. Cornell University’s funding was partially limited; its main campus in Ithaca remained restricted, but its New York City-based Weill School of Medicine was able to draw down some funds. The University of Pennsylvania received funds after settling on July 1, while Princeton University continued to get NIH payments without DOGE restrictions. Duke University and UCLA, targeted in the most recent round of cuts, received NIH disbursements in August for expenses incurred in July, but future funding remains uncertain.
Harvard, for its part, has been unable to access any NIH funds since April 2025, despite being awarded more than 140 grants with a combined multi-year value exceeding $60 million. The university received $488 million from the NIH in fiscal year 2024, accounting for over 70% of its federal funding. According to an August press release from Harvard’s School of Public Health, the NIH was “continuing to block disbursement of any funds to Harvard University.”
Behind the scenes, DOGE’s involvement has been extensive. The agency’s officials, including Edward Coristine (who left DOGE in June after an attempted carjacking in August left him injured), met with NIH grant management officers in April to demand changes to the grant process. DOGE’s control of the PMS has allowed it to act as a gatekeeper, quietly sidestepping court orders and using the payment process as leverage in negotiations with universities. As Samuel R. Bagenstos, a former general counsel for the Department of Health and Human Services, told The Crimson, “They do not have the right to use a grant review process to evade the District Court order. If this continues, it sure looks like something Judge Burroughs would want to look at for contempt.”
While the funding battles rage, the NIH itself faces deeper structural and cultural challenges. Large-scale reproducibility projects have revealed that many published experiments are questionable. For example, a project funded by philanthropist Stuart Buck found that replication experiments in cancer biology returned results 85% smaller than the original studies, with only 46% of findings replicating successfully. The agency’s own director of Alzheimer’s funding was recently fired for falsification, discovered not through internal oversight but by amateur online sleuths.
Proposals for reform abound. Buck, now executive director of the Good Science Project, suggests that the NIH should dedicate at least 1% of its budget—about $500 million—to systematic replication studies and fraud detection. He also argues for slashing the administrative burden on scientists, who currently spend nearly half their time on compliance paperwork. “The NIH should lay out an ambitious goal to slash the administrative burden to 20% of researcher time within three years,” Buck wrote in STAT News. He advocates for using AI tools to track research progress and eliminating unnecessary progress reports, freeing up scientists to focus on actual discovery.
Another target is the NIH’s sprawling 27-institute structure, which critics say is a relic of decades-old bureaucratic growth rather than a reflection of modern medical science. Both congressional Republicans and the administration have proposed reorganizing the NIH into broader, more efficient offices—a move first suggested by former NIH director Harold Varmus in 2001. The Scientific Management Review Board, established by Congress in 2006 to advise on NIH’s optimal structure, was revived in November 2024 to tackle these questions anew.
Funding models are also under scrutiny. The NIH’s peer review system, which demands “preliminary data” to prove experiments will work, is seen as stifling innovation. Many Nobel laureates and top scientists say their groundbreaking work would not have been funded under current rules. Buck proposes eliminating preliminary data requirements and experimenting with new review mechanisms—such as rewarding proposals that spark strong disagreement among reviewers, or funding scientists who switch fields to bring fresh perspectives. He calls for a dedicated Center for Experimentation and Innovation within NIH to test these ideas at scale.
Finally, the NIH Common Fund, designed for cross-disciplinary research, has stagnated at $600-700 million annually since 2006. Buck and others urge tripling it to $2 billion to better address complex challenges like nutrition, aging, and chronic disease—issues that cut across traditional disease categories and require more systematic study.
While many of these reforms could be implemented administratively, the obstacles are political and cultural, not legal. The stakes are high: public trust in science is eroding, and bureaucratic dysfunction threatens to delay or derail research breakthroughs that could save lives. As the Trump administration continues to wield its new tools for oversight and leverage, the future of American biomedical research hangs in the balance—caught between calls for accountability and the risk of paralyzing the very engine of discovery it seeks to reform.
