The Trump administration has left billions of dollars that Congress appropriated for health programs unspent, and some funding could expire Wednesday when the fiscal year ends. Starting Oct. 1, hundreds of thousands of immigrants with legal status could also lose government health coverage under a law President Donald Trump signed. Decisions made at the top affect people who rely on care, research and local health programs.
Congress appropriated the money, but the administration held it back
Congress appropriated $9.4 billion for global health programs for fiscal 2026, preserving the President’s Emergency Plan for AIDS Relief (PEPFAR), the Global Fund to Fight TB, AIDS and Malaria, and HIV/AIDS programs previously administered through the U.S. Agency for International Development (USAID). The administration hasn’t spent $1.3 billion intended to protect maternal and child health and counter infectious diseases, including HIV/AIDS, malaria and tuberculosis.
Congressional leaders had warned for more than a month that the administration was holding back the money. Last week, Sen. Susan Collins (R-Maine), chair of the Senate Appropriations Committee, urged administration officials to spend it as intended.
Collins and top Democrats worry the administration is diverting the $1.3 billion for global health programs, along with $1.2 billion for development assistance, to pay for shutting down USAID. Lawmakers said another $725 million was due to expire Wednesday rather than be spent. It wasn’t clear whether Collins received a response after she asked administration officials how they would use the money.
Under the Trump administration’s “America First” foreign aid program, the United States is entering bilateral agreements with individual countries so they can eventually rely less on U.S. funding. Late last week, the White House also unilaterally canceled nearly $1 billion in funding Congress had appropriated. Democratic and some Republican lawmakers say withholding the money is illegal.
Local programs lose money and work
Congress passed $101 million for the Teen Pregnancy Prevention (TPP) program, but the Department of Health and Human Services (HHS) has spent only about $500,000. Created in 2010, the evidence-based program funds organizations that help young people make healthy decisions, reduce sexual risk behavior, and decrease sexually transmitted infections and unintended teen pregnancy.
In June, HHS abruptly terminated 53 grants to nonprofits, universities and health departments, worth about $67 million, two years before they were due to expire. HHS said the grants no longer aligned with agency priorities, and the administration wanted to reshape TPP into abstinence-only curricula. A list seen by The Hill said HHS terminated most grants because it said they normalized or promoted sexual activity for minors.
In August, a federal judge blocked the administration’s changes to TPP while a lawsuit proceeds. U.S. District Judge Christopher Cooper said he wasn’t sure he had authority to reinstate the canceled grants, and a decision on that question is pending. In a letter to HHS, 92 House and Senate Democrats led by the Democratic Women’s Caucus said the administration hadn’t restored any funding. Local programs working to reduce teen pregnancy, sexually transmitted infections and other health risks for young people had halted work.
“HHS’s only options are to either return the funding to the communities and teens who rely on it or let it go to waste,” the lawmakers wrote. President Trump’s 2027 budget request proposed eliminating the program, calling it leftist and ineffective, though he signed the fiscal 2026 budget into law with the funding included.
Research and coverage under pressure
Congress appropriated about $345 million for the Agency for Healthcare Research and Quality (AHRQ) this year. In July, AHRQ told researchers it was halting at least 104 grants across 32 states, many aimed at improving patient safety. Sens. Patty Murray (Wash.) and Tammy Baldwin (Wis.), top Democratic appropriators, said HHS told them it planned to award just 90 grants this year and sought to transfer $100 million specifically appropriated for AHRQ to other agencies.
At his confirmation hearing on Sept. 16, Chris Klomp, nominee for HHS deputy secretary, told senators AHRQ was “on track to expend 97 percent of its appropriated funds by the end of the fiscal year.” The article said that figure apparently didn’t reflect research grants. The White House had also failed to spend AHRQ funding before, impounding $80 million after it failed to award grants from fiscal 2025.
“We’ve seen almost no money go out the door, and so unless they actually somehow manage to ship it all out today or tomorrow, there’s going to be a massive impoundment at AHRQ, and likely the result will be lawsuits or hopefully further congressional action,” said Aaron Carroll, chief executive of AcademyHealth, a health services research group that supports AHRQ’s work. Carroll said AHRQ studies problems such as patients’ difficulty getting appointments and concerns about the quality of care.
Separately, state data shows hundreds of thousands of immigrants with legal status are at risk of losing government health coverage starting Oct. 1. The One Big Beautiful Bill ends Medicaid eligibility for refugees, asylees, trafficking victims and others. The effect may be greater than initially predicted. President Donald Trump signed the law on July 4, 2025, and it cuts more than $900 billion in Medicaid spending through 2034.