by Annie Waldman

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For more than two months, the Trump administration has been subject to a federal court order stopping it from cutting funding related to gender identity and the provision of gender-affirming care in response to President Donald Trump’s executive orders.

Lawyers for the federal government have repeatedly claimed in court filings that the administration has been complying with the order.

But new whistleblower records submitted in a lawsuit led by the Washington state attorney general appear to contradict the claim.

Nearly two weeks after the court’s preliminary injunction was issued, the National Institutes of Health’s then-acting head, Dr. Matthew J. Memoli, drafted a memo that details how the agency, in response to Trump’s executive orders, cut funding for research grants that “promote or inculcate gender ideology.” An internal spreadsheet of terminated NIH grants also references “gender ideology” and lists the number associated with Trump’s executive order as the reason for the termination of more than a half dozen research grants.

The Washington attorney general’s allegation that the Trump administration violated a court order comes as the country lurches toward a constitutional crisis amid accusations that the executive branch has defied or ignored court orders in several other cases. In the most high-profile case so far, the administration has yet to comply with a federal judge’s order, upheld unanimously by the Supreme Court, requiring it to “facilitate” the return of Kilmar Armando Abrego Garcia, who was mistakenly deported to El Salvador in March.

The records filed in the NIH-related lawsuit last week also reveal for the first time the enormous scope of the administration’s changes to the agency, which has been subject to massive layoffs and research cuts to align it with the president’s political priorities.

Other documents filed in the case raise questions concerning a key claim the administration has made about how it is restructuring federal agencies — that the Department of Government Efficiency has limited authority, acting mostly as an advisory body that consults on what to cut. However, in depositions filed in the case last week, two NIH officials testified that DOGE itself gave directions in hundreds of grant terminations.

The lawsuit offers an unprecedented view into the termination of more than 600 grants at the NIH over the past two months. Many of the canceled grants appear to have focused on subjects that the administration claims are unscientific or that the agency should no longer focus on under new priorities, such as gender identity, vaccine hesitancy and diversity, equity and inclusion. Grants related to research in China have also been cut, and climate change projects are under scrutiny.

Andrew G. Nixon, the director of communications for the Department of Health and Human Services, the NIH’s parent agency, told ProPublica in an email that the grant terminations directly followed the president’s executive orders and that the NIH’s actions were based on policy and scientific priorities, not political interference.

“The cuts are essential to refocus NIH on key public health priorities, like the chronic disease epidemic,” he said. Nixon also told ProPublica that its questions related to the lawsuit “solely fit a partisan narrative”; he did not respond to specific questions about the preliminary injunction, the administration’s compliance with the order or the involvement of DOGE in the grant termination........

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