A federal judge on Friday regained billions of dollars in grants, setting the almost certain appeal, by permanently limiting funds from the National Institutes of Health, which supports research at universities and academic medical centers.
The decision by Massachusetts U.S. District Court Judge Angel Kelly was one of the first final decisions in the barrage of lawsuits against the Trump administration, which issued her permanent, previous temporary order. But it happened in an unusual way. The government asked the court to enter such a ruling on Friday, allowing the appeal to proceed.
Nevertheless, this decision was the first victory in the assortment of diverse institutions conducting medical research. After the Trump administration announced policy changes in February, many research hospitals and universities issued disastrous warnings that the proposal threatened America's scientific capabilities and innovation, and estimated that the changes could raise nearly $4 billion shortfalls for these agencies.
Under the Trump administration's plan, the National Institutes of Health was able to obtain funds to provide to cover the “indirect costs” of research, such as the maintenance of buildings, utilities and support staff. Historically, when agencies awarded grants, they could, in some cases, allocate nearly 50% to cover indirect costs associated with a particular study.
The Trump administration said it had seen the policy as a direct payment method, covering scientists' salaries and purchasing the necessary equipment, in contrast to the many tangential costs that hospitals and labs maintain facilities and other overhead costs, to directly pay more federal dollars.
However, critics said the changes proposed by the administration would paradoxically force the system to cover the bill, cutting staff in the process and expanding research projects.
At the February hearing, the lawyer explained that he would be forced to abandon the dizzy lab under construction and clinical drug trials that are ongoing if he had to cover overnight more or less overhead costs himself.
Judge Kelly has consistently agreed, repeatedly rulings that the policy appears to be unnecessary and reckless, and repeatedly rulings that it would cause serious harm to important medical research. Initially, after the Trump administration banned the changes in February, she extended the order twice while the lawsuit was unfolding.
The government wrote that the incident presented “negative legal issues.”
The decision comes as the scientific research community tackled a deeper threat to the Department of Health and Human Services from recent avalanche cuts. Many of the grant officers from the National Institutes of Health and other departments appeared to have been wiped out by those layoffs.
Earlier on Friday, the 16 state coalition sued the Trump administration over withholding grants that cover the direct costs of medical research, claiming that they were also suspended, putting those states at a more explicit risk.

