Elle Saine, MD, PhD, MA, had a federal guideline on sexually transmitted infections open on her laptop last January when the link suddenly went dark. Now, the recommendations are back, but Saine’s confidence in government websites is shakier than it was before.

Federal agencies took scores of pages of health information offline last year to comply with President Donald Trump’s executive order on what was described as “gender ideology.” Some physicians and groups, including Doctors for America, filed lawsuits to restore the information.

Those legal battles have forced hundreds of pages back online, and key datasets are up and running.

Some links remain broken, and some datasets have stalled or dropped measures related to gender identity. At the same time, changes to vaccine information have driven many physicians to turn to professional societies and other sources for guidance.

“There are things that I trust and things that I don’t trust anymore,” said Saine, infectious disease epidemiologist and vice chair of community health and prevention at Doctors for America. When reviewing federal information, she now checks when it was last updated. “We want to be able to rely on and trust the guidelines and the data that’s available to us.”

Trump’s January 2025 executive order stated that the two sexes are not changeable and directed federal agencies to use the term “sex” and not “gender.” Agencies also received instruction to remove media that “inculcate or promote gender ideology,” with a deadline of January 31 at 5 PM ET. A separate order instructed agencies to end programs related to diversity, equity, and inclusion.

The Department of Health and Human Services (HHS) is following Trump’s executive orders, said HHS Press Secretary Emily Hilliard in an email.

Webpages on HIV care, contraception, adolescent health, and more were pulled, alarming physicians who relied on them in their practices and research. An estimated 13% of CDC databases were removed between January 21 and February 11, a New England Journal of Medicine analysis found.

Ongoing Legal Challenges

The medical advocacy group Doctors for America filed a lawsuit, alleging that the sudden removal violated the Administrative Procedure Act, which states that the government can’t take actions that are “arbitrary, capricious,” or otherwise unlawful. The group also argued that the government violated the Paperwork Reduction Act, requiring timely access to public information and warning when substantially changing or removing significant information. The City of San Francisco later joined the case.

The Washington State Medical Association (WSMA), the Washington State Nurses Association, and other groups filed a similar lawsuit. In March 2025, two Harvard doctors challenged the removal of their papers, which included references to LGBTQ patients, from the Patient Safety Network (PSNet). That violated the First Amendment, they argued, by imposing an unreasonable, viewpoint-based restriction on a forum hosting private speech.

Earlier this month, the Harvard researchers’ legal counsel announced an agreement with the government, requiring that the papers stay online. The agreement also prohibits other PSNet papers from being taken down for the same reasons, according to the American Civil Liberties Union (ACLU), which represented the doctors. “It reflects a huge win for the First Amendment and public health in general,” said Scarlet Kim, JD, senior staff attorney at the ACLU.

A federal judge in July ruled in favor of Doctors for America, requiring that certain pages flagged by the group be restored. A total of 195 webpages are back online, the group said, including pages on the Health Insurance Portability and Accountability Act of 1996 and reproductive health, HIV care guidelines, and hormonal contraceptives. Twenty-seven pages were not subject to the order. The government settled the case with the WSMA in September, restoring 33 webpages, the association said. Sixteen other pages fell outside its scope.

Many restored pages display a yellow banner stating any information promoting “gender ideology” is inaccurate. “This page does not reflect reality, and therefore the Administration and this Department reject it,” it reads.

A CDC webpage with HIV information for transgender patients, an FDA page on health equity and artificial intelligence, and other links also remain offline. Because only a few hundred specific pages were identified in court filings, it is unclear how many pages overall are still down or how reliable new information will be, said Andrew Twinamatsiko, JD, co-director of the Center for Health Policy and Law at the O’Neill Institute at Georgetown University, Washington, DC.

Outside of the cases, datasets including those on virus-associated hospitalizations remain active. PopHIVE, a Yale School of Public Health data project, still uses datasets from the CDC and other agencies, comparing them with other data streams where possible. Some datasets that researchers and public health experts worried might not update, such as the local-level PLACES data tool, have published, she said.

“There’s been a lot of uncertainty; I would say probably more uncertainty than there actually has been change,” said Anne Zink, MD, Yale senior fellow who works on PopHIVE.

Still, Zink has run into issues. Past data on US syphilis rates disappeared after Zink planned to use it in an upcoming paper. She ultimately cited CDC Restored, an independent project that archived the CDC website.

Without historical data, Zink said, “You lose so much context.”

Between January 20 and March 25, 2025, some 49% of 232 HHS datasets were altered, one report found. Most switched the word “gender” to “sex,” a change that could undermine the data’s interpretation, the authors wrote. Another recent review found at least one measure of gender identity or sexual orientation had been removed from 360 federal data collections, including surveys, surveillance systems, and government-funded studies.

CDC Pauses Publication of Some Data

Some CDC datasets also paused publishing new data, according to a recent paper in the Annals of Internal Medicine. As of October 28, 2025, 38 out of 82 datasets that had previously updated at least monthly had been paused. Thirty-four of them had posted no data in the prior 6 months. Most paused databases were vaccine-related.

“There’s nobody else who is going to be able to produce data with the same reach and breadth,” said Janet Freilich, JD, law professor at Boston University, Boston, and senior author on the paper, who noted that some datasets have since been updated. “If the federal government’s not doing this, it just leaves an information gap.” The uncertainty surrounding the data, coupled with actions including unilaterally changing the childhood vaccine schedule, has undermined trust in federal information, doctors said.

“The websites are up, but no one looks at them anymore,” said John Bramhall, MD, past president of the WSMA. “A terrible blow has been dealt to the authority and reputation of a variety of US government sources of information.”