Congress used the power of the purse to reverse RFK Jr.'s cuts to CDC, FDA, and NIH

On February 3, 2026, President Trump signed the FY2026 Consolidated Appropriations Act, which contained the Labor-HHS-Education division that directly governs CDC, NIH, and FDA funding. The bill fully funded the CDC at $9.2 billion — rejecting RFK Jr.'s proposed $3.6 billion cut — fully funded NIH at $49 billion (an increase over FY2025), and funded the FDA at enacted levels, rejecting proposed reductions.

The House passed the broader funding package 217-214 on a largely party-line vote; the Senate voted 71-29 on a five-bill package that was then merged in conference. The bipartisan 71-29 Senate margin reflected that enough Republican senators from states with major research universities, NIH-funded medical centers, and pharmaceutical manufacturing — 🌽Iowa, 🏜️Utah, 🔔Pennsylvania, 🦞Maine — broke with the administration's proposed cuts.

The legislation went well beyond dollar amounts. Senate Appropriations Labor-HHS Subcommittee Ranking Member Tammy Baldwin (D-WI) negotiated statutory provisions that write specific operating requirements into law rather than merely allocating money. These provisions: (1) require HHS to maintain staffing levels 'sufficient to carry out programs funded in this Act' — making workforce reductions at funded agencies a potential statutory violation rather than a purely executive decision; (2) prohibit HHS from implementing the Administration for a Healthy America reorganization RFK Jr. had announced, which would have folded the CDC, HRSA, SAMHSA, and other agencies into a new superstructure; (3) require the HHS Secretary to submit a detailed reorganization plan to both appropriations committees and make it publicly available at least 60 days before moving any CDC functions to another HHS component.

The AHA (Administration for a Healthy America) reorganization was RFK Jr.'s most ambitious structural initiative: a plan to dissolve the existing agency structure and merge chronic disease prevention functions from the CDC, SAMHSA, HRSA, and FDA into a new centralized 'AHA' with aligned leadership and a unified mission around 'Make America Healthy Again.' RFK Jr. announced the restructuring on March 27, 2025 without prior congressional consultation.

The FY2026 bill's prohibition — which bars implementation without the 60-day advance notice — effectively freezes the AHA reorganization for the duration of the appropriations year. A second round of notification and appropriations language would be required for FY2027.

The NIH funding figure — $49 billion — represented a roughly $1.7 billion increase over FY2025 enacted levels and a rejection of Trump's budget request, which had proposed cutting NIH by approximately $18 billion (roughly 37%)

The proposed cuts would have eliminated or drastically reduced funding for: Fogarty International Center (global health research); the National Institute on Minority Health and Health Disparities; grants for environmental health research at NIEHS; and peer-reviewed research on gun violence, climate-related health, and dietary science

Congress maintained all of these programs The $49 billion NIH figure made the U.S. the world's largest funder of biomedical research by a significant margin and preserved the infrastructure that produces approximately 30% of all peer-reviewed biomedical research cited worldwide.

The Impoundment Control Act of 1974 became the central enforcement mechanism for congressional intent in FY2026. The ICA prohibits the executive branch from withholding or deferring congressionally appropriated funds without following specific procedures — it was passed after President Nixon impounded funds he disagreed with.

The Trump administration had already triggered ICA concerns: GAO found the administration had illegally impounded $26 billion in transportation and education funds in April 2025 and opened 39 separate impoundment investigations. If the administration attempted to impound HHS funding appropriated in the FY2026 bill — whether by freezing NIH grant disbursements, refusing to hire the staff required to maintain programs, or letting existing contracts lapse without renewal — it would face ICA violations on top of potential contempt of court orders from ongoing DOGE-related litigation.

The $9.2 billion CDC figure preserved the agency's core epidemiological surveillance, laboratory, and data functions — but did not restore the staffing and contracts already eliminated before February 3. Between January and December 2025, the CDC lost approximately 2,000 employees through layoffs, buyouts, and forced resignations.

CDC Director MBMatthew Buzzell stated in January 2026 that the agency was 'operating at reduced capacity in several program areas' and could not commit to fully restoring paused surveillance systems without additional hiring authority. The 60-day reorganization notice requirement gave Congress a window to respond if RFK Jr. attempted to redirect CDC funding to new structures — but it did not automatically restore what had already been cut before the appropriations bill was signed.

The 217-214 House vote reflected the narrowness of Republican control in the lower chamber and the difficulty of assembling majorities for appropriations bills that maintain funding levels the administration opposed. Seven House Republicans voted against the bill — primarily hardline members who wanted deeper cuts — while no House Democrats voted for it.

Speaker MJMike Johnson managed the vote with zero margin for error. The razor-thin majority means any future confrontation on FY2027 appropriations will be at least as difficult — and the administration's ability to propose deeper HHS cuts in its FY2027 budget request sets up a near-identical legislative battle beginning in the fall of 2026.

The FY2026 appropriations process also addressed DOGE's activities at HHS agencies. Language in the final bill prohibited: HHS from allowing any employee or detailee whose primary employment was outside the agency to access confidential public health data or grant review materials without written authorization from the Secretary and a 30-day advance notice to the relevant appropriations committee; and the use of appropriated funds for any DOGE activity not authorized in writing by the Office of Personnel Management and the Office of Management and Budget. These provisions were the first statutory constraints on DOGE activity written into an appropriations bill — a recognition by appropriators that DOGE's access to agency data and grant systems had occurred outside any established legal framework.