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In his first months in office, President Trump has slashed funding for medical research, threatening a longstanding alliance between the federal government and universities that helped make the United States the world leader in medical science.

Some changes have been starkly visible, but the country’s medical grant-making machinery has also radically transformed outside the public eye, a New York Times analysis found. To understand the cuts, The Times trawled through detailed grant data from the National Institutes of Health, interviewed dozens of affected researchers and spoke to agency insiders who said that their government jobs have become unrecognizable.

In all, the N.I.H., the world’s premier public funder of medical research, has ended 1,389 awards and delayed sending funding to more than 1,000 additional projects, The Times found. From the day Mr. Trump was inaugurated through April, the agency awarded $1.6 billion less compared with the same period last year, a reduction of one-fifth. (N.I.H. records for May are not yet comparable.)

The impacts extend far beyond studies on politically disfavored topics and Ivy League universities like Columbia or Harvard. The disruptions are affecting research on Alzheimer’s, cancer and substance use, to name just a few, and studies at public institutions across the country, including in red states that backed Mr. Trump.

“I think people should know that research that they probably would support is being canceled,” said Eden Tanner, a chemist at the University of Mississippi, who had been working with a colleague at Ohio State University to develop a novel approach for treating glioblastoma, an aggressive form of brain cancer. Their grant had been awarded through a program designed to diversify the biomedical workforce; in April, they were notified that it was being terminated.

“I would like to cure brain cancer,” Dr. Tanner said. “I think that’s not particularly controversial.”

Mr. Trump’s campaign against medical research has been carried out without congressional approval, and the legality is unclear. Lawsuits have challenged the slashing or delaying of funding.

Federal officials, who have accused the N.I.H. of wasteful spending, have attributed the cuts to changing scientific priorities.

The N.I.H. “regularly examines its research portfolio” to determine which projects are “the most meritorious,” Andrew Nixon, a spokesman for the U.S. Department of Health and Human Services, said in an email. “Regular reviews of ongoing activities will help us determine the most strategic balance of projects to support and the best way to manage them going forward, especially as we need to be responsive to the often-changing nature of biomedical scientific progress.”

Scientists fear that the sweeping cuts could do long-term damage to U.S. scientific research, which has long driven medical and financial progress for the nation. “The country is going to be mourning the loss of this enterprise for decades,” said Dr. Harold Varmus, a Nobel Prize-winning cancer biologist who served as the director of the N.I.H. during the Clinton administration and the director of the National Cancer Institute under President Barack Obama.

N.I.H. grants, awarded in a competitive process, are typically paid out in installments. A researcher with a $1 million four-year grant, for instance, will get about $250,000 a year. Scientists can use this money to buy equipment and supplies and to pay the salaries of the researchers who work in their labs, among other things.

From 2015 to 2024, there have been fewer than 20 terminations a year, on average, according to Jeremy M. Berg, former director of the National Institute of General Medical Sciences at the N.I.H. from 2003 to 2011. They were generally for extenuating circumstances, such as illness or research misconduct.

But since late February, the government has publicly announced the cancellation of 1,389 N.I.H. awards. The agency scoured grants for key words and phrases like “transgender,” “misinformation,” “vaccine hesitancy” and “equity,” ending those focused on certain topics or populations, according to a current N.I.H. program officer, who asked not to be identified for fear of retribution.

Studies focused on sexual and gender minority groups were among the first on the chopping block.

Katherine Bogen, a doctoral student at the University of Nebraska-Lincoln, had been studying post-traumatic stress, alcohol use and intimate partner violence against bisexual women. The termination notice she received assailed studies “based primarily on artificial and nonscientific categories,” calling such research “antithetical to the scientific inquiry” and alleging that it was “often used to support unlawful discrimination on the basis of race and other protected characteristics, which harms the health of Americans.”

The language was “very insulting,” she said. “I get this letter that tells me, ‘Your research is not science. Not only is it ascientific, it’s a useless drain on resources, and, in fact, your research could be used to discriminate against ‘actual’ Americans or ‘regular’ Americans,’ or whatever they mean.”

The cuts spread to grants on health equity and racial and ethnic groups. Affected projects sought to improve access to mental health care for Latino, low-income and rural communities; to reduce maternal mortality among Black women; and to prevent gun violence in Asian American communities.

Tsu-Yin Wu, a researcher at Eastern Michigan University who led the gun violence project, said that community leaders and study participants were “greatly disappointed” by the grant cancellation. “Some felt betrayed that their voices and engagement no longer matter.”

The agency cut grants for research on vaccine hesitancy, disinformation and misinformation, including a Northeastern University study on cancer misinformation on social media.

It also axed research on Covid-19, including studies that could have helped the nation respond to many infectious disease threats. Among them: a grant to Emory University and Georgia State University, where researchers had developed three potential drugs that showed promise against many RNA-based viruses, including coronaviruses, Ebola, avian influenza and measles, said George Painter, a pharmacologist at Emory who was co-leading the research.

In April, the agency terminated, in part or in whole, more than 350 grants meant to support students, early-career scientists or researchers from groups underrepresented in science. Among these terminations were F31 diversity grants, awarded to Ph.D. students who were members of certain racial or ethnic groups, disabled or from disadvantaged backgrounds.

At the University of Pittsburgh, Luzmariel Medina-Sanchez, who was born and raised in Puerto Rico, and Sierra Wilson, a first-generation college student from Utah, both had their grants canceled. “It’s not even about the work I’m doing,” said Ms. Wilson, who studies how liver cells respond to drug overdoses. “It feels like it’s about me.”

Ms. Medina-Sanchez, who studies how a microbe can help treat celiac disease, said she may leave science altogether. “I feel racially targeted,” she said. “I feel like I’m not going to be a professional in the field of science in America, because obviously my name is Luzmariel.”

(Ms. Wilson and Ms. Medina-Sanchez stressed that they spoke only for themselves and not for the university.)

Besides outright canceling projects, N.I.H. failed to distribute annual payments to more than 1,000 grants, The Times found.

The delays have stifled research on drug discovery, blood vessel health and injury response. In some cases, scientists have cut staff, paused hiring, trimmed back supplies or delayed experiments. Health officials have not explained which projects have been held up, why or for how long.

The Times compiled a list of the delayed grants by searching N.I.H. databases as of June 2 for ones that were funded in 2024 and expected to last beyond 2025, but have not gotten disbursements on schedule.

In the past, annual renewals were routine. Scientists submitted progress reports; the N.I.H. reviewed them and usually continued funding them, occasionally with a week or two of delays. But longer delays have become much more common since Mr. Trump took office.

Joshua Kritzer, a professor of chemistry at Tufts University, investigates the basic science behind potential drug candidates, laying the groundwork for future medications. Most of his lab work is supported by a five-year N.I.H. grant that received $1.4 million over the past two years. But since February, he had been waiting for the third year of expected funding to come in. He slashed purchases of essential supplies and contemplated laying off crucial researchers on his team.

On Tuesday, Kritzer finally received word that his funding had been released, several days after The Times asked federal officials about his and other delayed awards.

“Every week that’s delayed, it’s easily probably three to four weeks to get that research back to where it was,” said Dr. Kritzer, who noted that he was speaking for himself and not for his institution.

Mr. Nixon, the Department of Health spokesman, said that the agency would not discuss deliberations about specific awards but encouraged grant recipients to “speak with the designated N.I.H. officials on their award notice when questions arise.”

In some cases, delays have lasted so long that scientists wondered whether their grants were subject to a “shadow termination.”

The delays stem in part from additional screening for whether the grants align with Trump administration priorities, N.I.H. officials said. Other renewals have been delayed as overstretched N.I.H. staff members work through backlogs in funding. And political appointees are now vetting some projects, too, slowing the process further.

N.I.H. officials said they feared being fired if they processed a grant renewal that the administration disfavored.

In early May, Jon Lorsch, a longtime N.I.H. institute director who was recently promoted to acting deputy director of the agency’s external funding arm, emailed staff members denouncing the renewal of grants “that focused on topics that are not supported under N.I.H./H.H.S.’s priorities,” according to a copy of the email seen by The Times.

“The consequences of approving an award that should not have been approved could be very serious,” he wrote.

But Courtney Griffin, who leads a lab at the Oklahoma Medical Research Foundation and studies blood vessel development and disease, including complications due to diabetes, expressed confusion as to why her expected funding is not coming through. She and her colleagues were making contingency plans and looking for other sources of funding.

“It’s, ironically, a really inefficient use of people’s time to be in this guessing game,” she said, adding that the time could be better spent on biomedical research.

Months-long delays are also affecting new grants that were being vetted when the Trump administration cracked down on grant reviews.

A number of major Alzheimer’s Disease Research Centers, some of which have operated for decades, have waited months for the Trump administration to decide whether to award them fresh five-year grants. The funding gaps have set back ongoing studies and curtailed efforts to take images of patients’ brains, though the N.I.H. has recently told some centers that they would soon receive funding.

“These centers have become a safety valve for people who can’t get a neurology appointment at a private center,” said Dr. Ann Cohen, a co-director of the University of Pittsburgh Alzheimer’s center. Now, she said, things have changed. “There are fewer clinic appointments, fewer opportunities for these individuals to get brain imaging.”

The N.I.H. has also said that it will no longer fund projects in which U.S. researchers distribute some of their money to international partners, throwing the future of many global health projects into question and creating funding delays for ongoing research.

Beyond the disruption of individual projects, other proposed changes could undermine scientific research across the board, experts said. One would sharply curb funding for indirect research costs, such as building maintenance and administrative staff. And then there is Mr. Trump’s proposal to slash the N.I.H.’s total budget by about $18 billion, a cut of almost 40 percent.

A budget cut of that scale would be “truly draconian,” said Dr. Varmus, the former N.I.H. director, who said he hoped Congress would not approve such a sharp reduction. It could leave the agency without enough money to fund promising new work, drive some scientists overseas and prompt some up-and-coming researchers to leave science altogether, he said. “You can completely destroy the system in just a couple of years,” Dr. Varmus said.