Several institutions share the job of overseeing the FDA: the Department of Health and Human Services sits directly above it, the White House controls appointments and reviews its major rules, Congress funds and investigates it, the federal courts review its decisions for legal authority, and any member of the public can petition the agency on the record. No single office runs the show, and that dispersal is deliberate.
The Department of Health and Human Services
The FDA is housed inside HHS, and the HHS Secretary is the Commissioner’s direct superior in the federal chain of command.1U.S. Food and Drug Administration. FDA Organization Federal statute makes the point explicit: the Secretary, “through the Commissioner,” is responsible for executing the food and drug laws.2Office of the Law Revision Counsel. 21 U.S. Code 393 – Food and Drug Administration The Commissioner handles day-to-day work — drug reviews, food inspections, device approvals — while the Secretary sets broader health-policy priorities. The Secretary can, and on rare occasions has, overruled an FDA scientific recommendation outright; in 2011, the Secretary blocked the agency’s decision to allow over-the-counter access to an emergency contraceptive for all ages.
Placement inside HHS also means FDA budget requests, policy announcements, and regulatory proposals pass through the department before reaching the White House or Congress. HHS acts as a filter to keep agency-level decisions aligned with the administration’s public-health strategy.
The HHS Office of Inspector General
A separate watchdog inside HHS, the Office of Inspector General, has independent authority to audit and investigate the FDA. The OIG hunts for fraud, waste, and mismanagement across every HHS agency and publishes a rolling Work Plan flagging specific programs for review.3U.S. Department of Health and Human Services Office of Inspector General. Home Recent projects targeting the FDA include an audit of the agency’s oversight of dietary supplements and mandatory reviews of how the FDA accounts for national drug-control program funds.4U.S. Department of Health and Human Services Office of Inspector General. Browse Work Plan Projects OIG findings can trigger internal reforms, congressional hearings, or criminal referrals.
The President and the White House
The President nominates the Commissioner of Food and Drugs, and the nominee must be confirmed by the Senate before taking office.2Office of the Law Revision Counsel. 21 U.S. Code 393 – Food and Drug Administration Confirmation gives senators a chance to question a nominee’s qualifications and policy positions on the record. Because the Commissioner serves at the pleasure of the President, a new administration can replace agency leadership and change direction quickly.
OMB Review of Major Rules
Before the FDA can finalize a major regulation, the Office of Information and Regulatory Affairs (OIRA), a division of the White House Office of Management and Budget, reviews it for economic impact and consistency with administration priorities. Under Executive Order 12866, any proposed rule likely to have an annual economic effect of $100 million or more is classified as “economically significant” and receives heightened scrutiny.5GovInfo. Executive Order 12866 – Regulatory Planning and Review OIRA can send a rule back for revision if it finds costs outweigh benefits or if the rule conflicts with other federal objectives.
Ethics and Conflict-of-Interest Rules
Federal ethics regulations apply to every FDA employee, from an entry-level reviewer up to the Commissioner. The rules, codified at 21 CFR Part 19, prohibit employees from accepting favors or benefits that could appear to influence their official duties.6eCFR. 21 CFR Part 19 – Standards of Conduct and Conflicts of Interest Former FDA employees face additional restrictions, and in some cases permanent bars, on representing outside parties in matters they personally handled while at the agency. The point is to blunt the revolving door between the FDA and the industries it regulates.
Congress
Congress controls the FDA’s funding and has broad authority to investigate its operations. The annual appropriations process sets how much money the agency receives and can steer dollars toward specific programs or away from them. Financial leverage is one of the most powerful accountability tools lawmakers have.
Committees and Hearings
Two committees carry most FDA-related legislation and oversight: the House Committee on Energy and Commerce, through its Subcommittee on Health, and the Senate Committee on Health, Education, Labor, and Pensions. They hold public hearings where FDA officials answer questions on drug safety failures, food-inspection delays, and other agency work. When voluntary cooperation falls short, committees can subpoena internal documents and sworn testimony.
The Government Accountability Office
The Government Accountability Office is Congress’s independent auditor. GAO reviews FDA programs, tracks how the agency spends its budget, and evaluates whether it meets performance goals.7U.S. GAO. Overseeing Food and Drug Safety is Getting Harder at FDA A 2025 GAO report examined the FDA’s drug-inspection workforce and found that postponed surveillance inspections had created a backlog affecting the agency’s ability to prioritize facilities by risk.8Government Accountability Office. Drug Safety: FDA Should Implement Strategies to Retain Its Inspection Workforce GAO recommendations often push the agency toward operational changes and can prompt legislation.
Reauthorization of User-Fee Programs
More than half of the FDA’s budget comes not from taxpayers but from fees paid by the companies it regulates.9U.S. Food and Drug Administration. FY 2026 FDA Budget Summary The largest program, the Prescription Drug User Fee Act (PDUFA), funds new-drug application reviews in exchange for FDA commitments to meet review timelines and report performance to Congress annually.10U.S. Food and Drug Administration. PDUFA Annual Reports and Plans Congress must reauthorize these fee programs periodically, and each reauthorization is a moment to renegotiate terms, add requirements, or tighten oversight.11U.S. Food and Drug Administration. Prescription Drug User Fee Amendments Critics argue user fees can pull the agency too close to industry priorities; the reauthorization cycle is the main structural check on that risk.
The Federal Courts
When someone believes the FDA has overstepped its legal authority or acted unfairly, the federal courts provide a final layer of accountability. The Administrative Procedure Act gives any person harmed by an agency action the right to challenge it in court.12Office of the Law Revision Counsel. 5 U.S.C. Chapter 7 – Judicial Review
Standing to Sue
Not just anyone can file. To bring a case in federal court, a plaintiff must show three things: a real or threatened injury, a link between that injury and the FDA’s action, and a likelihood that a court ruling would fix the problem. Disagreeing with an FDA policy is not enough on its own.
The Arbitrary-and-Capricious Standard
When a court reviews an FDA regulation or decision, it applies the standard in 5 U.S.C. § 706. A court will strike down an FDA action if the agency acted arbitrarily, exceeded its legal authority, ignored required procedures, or reached a decision unsupported by the evidence.13Office of the Law Revision Counsel. 5 U.S. Code 706 – Scope of Review The FDA must show a logical connection between what it considered and what it decided. Without that connection, a court can vacate the rule.
The End of Chevron Deference
For decades, courts gave the FDA and other agencies the benefit of the doubt when interpreting unclear statutes, a practice known as Chevron deference. That changed in June 2024, when the Supreme Court decided Loper Bright Enterprises v. Raimondo and overruled Chevron.14Supreme Court of the United States. Loper Bright Enterprises v. Raimondo Courts must now use their own independent judgment on whether an agency has acted within the authority Congress gave it, rather than deferring to any reasonable agency reading. In one early post-Loper Bright case, a federal court struck down an FDA rule that sought to regulate laboratory-developed tests as medical devices, finding the agency’s reading was not the best reading of the statute. Regulated companies no longer face the uphill battle of overcoming automatic deference, and more challenges to FDA regulations are expected.
Citizen Petitions
Oversight is not limited to government institutions. Any person, including non-citizens, can file a formal citizen petition asking the FDA to take a specific action: issue a new rule, change an existing regulation, or pull a product from the market. The process is governed by 21 CFR 10.30 and requires the petitioner to describe the requested action, lay out its factual and legal basis, and certify that the petition includes all relevant information, including anything unfavorable to the petitioner.15eCFR. 21 CFR 10.30 – Citizen Petition
Once filed, the FDA has 180 days to respond. The response can approve the petition, deny it, dismiss it if circumstances have changed, or explain why the agency needs more time.15eCFR. 21 CFR 10.30 – Citizen Petition Petitions can be filed electronically through regulations.gov or by mail. Individuals, consumer groups, and companies use the process to press for agency action, or inaction, on the public record.