WASHINGTON — The National Institutes of Health won’t be able to implement an across-the-board cap on how much it pays research universities and medical schools for indirect costs, under a federal court order released Wednesday in cases brought by Democratic attorneys general and university associations.
Judge Angel Kelley of the U.S. District Court of Massachusetts granted a nationwide preliminary injunction in the case, blocking the proposed 15% cap on Facilities and Administrative fees from taking effect while three lawsuits advance.
Those costs cover the expenses that go along with research, but that aren’t directly associated with one specific project. They can include construction, maintenance, equipment purchases, utilities and administrative staff.
Kelley wrote in the 76-page decision that a preliminary injunction would prevent the NIH from bringing about “immediate, devastating, and irreparable” harm to research institutions.
“First, the suspension of ongoing clinical trials and the resulting threats to patients’ lives represents a dire risk of a quintessentially irreparable nature. Second, the threats to non-human, yet still essential, research subjects similarly rings in irreparability,” Kelley wrote, referring to research animals. “Finally, the potential loss of human capital and talent to virtually every Plaintiff poses yet another harm incapable of run-of-the-mill legal relief.”
Kelley wrote that the “Court is hard pressed to think of a loss more irreparable than the loss of a life, let alone the thousands of people who are counting on clinical trials as their last hope.”
How suit came about
The NIH announced on a Friday in early February that it would no longer pay research universities and medical colleges the indirect cost percentage that each had negotiated with the federal government over the course of years.
Instead, NIH said it would cap Facilities and Administrative fees at 15% for every institution receiving funds from the NIH, producing an outcry from medical colleges and universities.
Three lawsuits were quickly filed, challenging the NIH’s decision: Commonwealth of Massachusetts v. National Institutes of Health, Association of American Medical Colleges v. National Institutes of Health and Association of American Universities v. Department of Health & Human Services.
All three were filed in the U.S. District Court of Massachusetts and assigned to Kelley, who was nominated by President Joe Biden and confirmed by the U.S. Senate in 2021 following a 52-44 vote.
Kelley quickly blocked the NIH from implementing the percentage change in the 22 states whose Democratic attorneys general filed one of the lawsuits, before entering a nationwide temporary restraining order in the case brought by the Association of American Medical Colleges.
Kelley held a hearing in late February to hear from the organizations that filed the three lawsuits and the Trump administration’s attorney over whether to issue a preliminary injunction.
Congress rejected earlier cap
The ruling released Wednesday notes that in 2017, during President Donald Trump’s first term in office, he sent Congress a budget request that asked lawmakers to set the NIH’s indirect cost rate at 10%.
Lawmakers, on a bipartisan basis, rejected Trump’s proposal and instead added language to the NIH’s annual spending bill that barred it from changing the percentage across the board. The language has been kept in the annual funding bill ever since.
“Congress’ rebuke of the first Trump Administration’s proposal to slash and cap was patently clear,” Kelley wrote. “This rider contains three, overlapping provisions meant to restrict NIH’s ability to enact an across-the-board rate reduction.”
Kelley wrote the preliminary injunction would “preserve public health, and by extension, serve the public interest.” She also wrote that the ruling would require the NIH “to abide by existing law and regulations.”
“It is impossible to accurately measure or compensate humans who lose their lives from a pause in research. It is impossible to measure the value of lost research animals—representing years of study central to medical breakthrough—that will be euthanized,” Kelley wrote. “It is impossible to measure the value of discovery from scientists who choose to leave, or of the potential students who now never become scientists at all.
“Even for those harms (that) can be measured in dollars and cents, the losses are compounding and will result in even greater disruption to ongoing research and clinical trials. As a result, failure to grant a preliminary injunction would certainly result in irreparable harm.”
This story was first published March 5, 2025 by States Newsroom.