The Government Is Shutdown, Now What?

Congress has failed to avert a government shutdown. The Department of Health and Human Services (HHS) is expected to face significant workforce reductions across its major agencies, though critical health programs may remain in place.

Centers for Disease Control and Prevention (CDC): About 36 percent of CDC employees would continue working, allowing the agency to respond to urgent disease outbreaks. Mandatory programs would not be affected, including the Vaccines for Children Initiative, which provides free immunizations to uninsured and underinsured children, and the World Trade Center Health Program, which offers care for people impacted by the 9/11 attacks.

National Institutes of Health (NIH): Roughly a quarter of NIH’s staff would remain on the job. The agency’s flagship research hospital, the NIH Clinical Center, would keep operating, ensuring continuity of patient care. However, much of the basic scientific research conducted by NIH scientists would be put on hold until funding resumes.

Centers for Medicare and Medicaid Services (CMS): Medicare benefits would continue uninterrupted, and Medicaid would be funded through the first quarter of fiscal year 2026 under the agency’s contingency plan. Essential staff would also remain in place to process payments under the Children’s Health Insurance Program (CHIP). More than half of CMS employees would keep working, but policymaking and oversight of contractors would likely be suspended. CMS has a posted contingency plan that details plans during the shutdown.

Food and Drug Administration (FDA): The FDA is expected to continue most of its operations, with 86 percent of staff retained. User fees would allow the agency to proceed with reviewing and authorizing new medical products, while also supporting work to ensure patient access to new therapies. Emergency response activities, such as managing recalls, would also continue.