Lukas Flippo

On Monday, a federal judge in Boston issued an order temporarily blocking the National Institutes of Health’s decision to cap indirect cost research reimbursements in 22 plaintiff states, including Connecticut. 

The injunction, issued after attorneys general from 22 states sued NIH, prevents the cuts from taking effect while the court evaluates the lawsuit, a move that legal experts say signals skepticism about the NIH’s abrupt rule change. The next hearing date is scheduled for Feb. 21. 

A second lawsuit, filed by private universities and hospitals, including MIT, Brown University and University of Pennsylvania, seeks to block the NIH’s decision nationwide. Yale has not joined the lawsuit filed by universities but issued a statement of support for the lawsuit filed by attorneys general.

“Donald Trump is defunding cancer research. He is defunding treatment for heart disease. He wants to defund research into autism, Alzheimer’s, and preventable newborn deaths,” Connecticut Attorney General William Tong wrote in a statement. “He wants to make us all sicker, and we cannot let him.”

University President Maurie McInnis condemned the NIH’s decision in a University-wide email, warning that the cuts posed a significant threat to Yale’s research and broader scientific innovation. She said that Yale was actively working with peer institutions and lawmakers to oppose the policy while preparing contingency plans to mitigate its potential impact.

At issue are indirect costs, which fund the infrastructure necessary for scientific research but are not tied to any single project. These costs cover lab maintenance, research facilities, administrative staff, utilities and compliance with federal regulations — expenses essential to keeping research institutions operational. 

The rates of indirect expenses reimbursement vary depending on an institution’s infrastructure needs. Yale currently has a federally negotiated Facilities and Administrative rate of 67.5 percent, which has been in place since 2016. The NIH’s new flat 15 percent cap significantly reduces the amount of funding institutions receive for essential overhead costs.

Universities warn that this change could force them to absorb the financial burden, reduce research programs or shift costs onto researchers themselves — potentially slowing scientific progress and limiting opportunities for early-career scientists.

“This decision poses a considerable threat to Yale’s research endeavors, which lead to medical breakthroughs, support patients in clinical trials, and drive economic growth,” McInnis wrote in a statement to the Yale community.

According to McInnis, indirect cost reimbursements help sustain over 2,000 research trials at Yale, supporting facilities that let more than 38,000 patients participate in clinical studies. Among these, 280 trials focus on cancer therapy, 80 involve mental health and behavioral care and 50 are related to heart disease.

In fiscal year 2024, Yale invested $432 million in research — more than double the amount received in indirect cost reimbursements from the NIH. However, most of Yale’s endowment is legally restricted to specific uses, so it cannot simply replace lost NIH funds.

“If we lose the support for a lot of that research on the margin, some research will no longer be performed. Some graduate students, postdocs, and faculty will not be hired,” said Howard Forman, a professor of radiology, public health, economics and management at Yale. “Some investments in faculty will not be made, some staff will be laid off. It’s not like the money will manifest itself from some other magical source.”

McInnis stated that Yale and more than 30 other universities have submitted public declarations in support of the second lawsuit. The University spokesperson did not immediately respond whether Yale considers joining the lawsuit. 

Additionally, Yale is actively working with peer institutions to explain to lawmakers that indirect costs are research costs and not administrative waste. 

Yale’s Office of the Vice Provost for Research has launched a 2025 Federal Administration Transition webpage, which requires a Yale NetID login, to provide updates on federal policy changes pertaining to Yale. 

The webpage reaffirms Yale’s commitment to opposing the NIH policy through legal, legislative and institutional efforts, while also preparing contingency plans to mitigate its impact. The site advises researchers to continue submitting grant proposals, but remain aware of potential delays in reviews and award disbursements.

The site also provides information on diversity, equity and inclusion, or DEI, funding restrictions, which have already been implemented by agencies such as the DOE, NASA and NSF. 

Connecticut, other states sue NIH

Connecticut joined 21 other states in suing NIH over the policy. 

“Without immediate relief, this action could result in the suspension of lifesaving and life-extending clinical trials, disruption of research programs, layoffs, and laboratory closures,” Connecticut Attorney General William said in a statement.

The lawsuit argues that NIH’s policy violates federal law by overstepping congressional authority, retroactively altering existing grant agreements and failing to follow established rulemaking procedures.

A 2017 spending law explicitly prohibits the NIH from making broad, categorical cuts to indirect cost reimbursements without legislative approval. Attorneys general claim that by applying the 15 percent cap to both new and active grants, NIH is forcing institutions to absorb unexpected financial losses on funding that had already been allocated.

The plaintiffs also argue that the policy change was enacted without following federal rulemaking procedures. NIH did not allow for stakeholder input before making the sweeping change, which the lawsuit claims was an arbitrary and capricious decision.

A U.S District Court judge Angel Kelley has temporarily blocked the NIH policy from taking effect in the 22 states that filed the lawsuit, allowing research institutions in those states to avoid immediate financial disruption. The court will now consider whether to grant a longer-term injunctions, which would prevent the policy from being implemented while litigation proceeds.  

Peer institutions grapple with changes

At the University of Connecticut, administrators are preparing for major financial shortfalls. According to UConn Vice President for Research Pamir Alpay, the university and UConn Health collectively received over $620 million in NIH funding this year.

Under the new policy, UConn expects to lose $35 million annually, forcing administrators to either cut research programs or find alternative funding sources.

The financial blow, Alpay explained, would likely affect ongoing and future research, particularly in areas reliant on NIH grants.

Research-intensive fields, including biomedical engineering, cancer treatment and neuroscience, face heightened uncertainty as administrators assess how to distribute increasingly limited resources.

Harvard President Alan Garber condemned the NIH policy in a statement as an “unprecedented attack on the nation’s research infrastructure.” 

At MIT, where NIH funding supports pioneering research in Alzheimer’s, Parkinson’s, Lyme disease and autism, the new policy could result in $30 to $35 million in annual losses. In response, MIT joined the second lawsuit to block the policy nationwide.

In an institute-wide email, MIT President Sally Kornbluth described the potential damage and the university’s legal action.

“To outsiders, capping the reimbursement rate for indirect costs at 15% might seem like a technicality. But ‘indirect costs’ are actually foundational to a thriving, world-class research enterprise,” Kornbluth wrote.

The loss of indirect funding, Kornbluth warned, could push universities into financial crises, potentially forcing them to halt research in crucial fields. 

The effects would extend beyond university walls, impacting the pharmaceutical and biotech industries, which rely on academic research for early-stage discoveries.

“We oppose these cuts because they will erode America’s global scientific leadership and deprive the American people of the fruits of research with untold potential benefits for their health and well-being,” Kornbluth wrote.

Yale received over $643 million in NIH funding in fiscal year 2024.

Correction, Feb. 11: Yale issued a statement supporting the lawsuit filed by attorneys general, not one brought by private universities and hospitals.