Since Robert F. Kennedy Jr. was confirmed as Secretary of Health and Human Services in February 2025, the FDA under RFK Jr. has lost roughly a fifth of its workforce, cycled through its top leader, rewritten childhood vaccine policy, and become the subject of active federal lawsuits over both the firings and the vaccine changes. The agency still approves drugs and inspects food plants, but it does so with about 16,600 employees instead of 19,000, under an acting commissioner, and with early data showing slower drug reviews and thinned-out food safety capacity.
How Much Smaller the FDA Is Now
The cuts started the day Kennedy was sworn in. On February 13, 2025, mass terminations of probationary FDA employees began across the agency, sweeping through teams working on nutrition, infant formula safety, food safety enforcement, and artificial intelligence research. Among those fired were 20 employees in the Office of Neurological and Physical Medicine Devices who had been reviewing clinical trial applications for Elon Musk’s Neuralink brain implant. Reporting at the time indicated that the Department of Government Efficiency, led by Musk, was directly involved in directing that first wave, including the Neuralink reviewers.1U.S. House Committee on Energy and Commerce (Democrats). Letter to HHS Secretary Kennedy Re: FDA Terminations
A larger, formal round came on March 27, 2025, when Kennedy announced a restructuring that would eliminate about 3,500 FDA positions, roughly 20 percent of the agency. HHS said the cuts targeted administrative functions such as policy, human resources, IT, procurement, and communications, and that drug reviewers, device reviewers, and food inspectors would be spared.2STAT News. HHS Job Cuts Include 3,500 FDA Layoffs The line held less well in practice. Forbes reported that more than 230 staff in the Human Foods Program were fired, including toxicologists and microbiologists; that nearly the entire Division of Food Processing Science and Technology was eliminated; that about 170 workers were cut from the Office of Inspections and Investigations; and that more than 140 were let go from the Center for Veterinary Medicine.3Forbes. FDA Job Cuts Spark Food Safety Debate
The process was widely described as chaotic. Badges were deactivated, mass emails arrived with little warning, and supervisors could not always identify which of their own staff had been let go. Kennedy himself acknowledged the disorder, saying as many as 20 percent of terminated employees might need to be brought back and that he had prioritized speed over precision to maintain “political momentum.”4NPR. RFK HHS Layoffs Restructuring The FDA later reversed terminations for roughly two dozen support staff.5BioPharma Dive. HHS FDA Restructuring Layoffs Tracker By early 2026, the agency had lost a total of 3,859 employees in 2025 and another 473 in 2026, bringing its headcount to approximately 16,602.6Food Navigator USA. FDA and USDA Staff Cuts Under Trump Raise Food Safety Risks
The layoffs were briefly blocked. In early July 2025, a federal district judge issued a preliminary injunction halting the reorganization, ruling it “likely unlawful.” The Supreme Court lifted that injunction on July 8, 2025, letting HHS proceed while noting it was “not commenting on the legality of each agency’s layoff plans.” Formal separation notices went out on July 14.7Fierce Biotech. HHS Terminates Employees After Supreme Court Allows Reduction in Force to Proceed
Who Runs the FDA Right Now
There is no permanent FDA commissioner. Dr. Marty Makary, a Johns Hopkins surgeon, was appointed in early 2025 and resigned on May 12, 2026, after 13 months. His tenure drew fire from both directions: Kennedy and allies faulted him for approving updated mRNA COVID-19 vaccines and a second generic mifepristone, while the pharmaceutical industry questioned the FDA’s predictability after what was described as a “U-turn” on Moderna’s mRNA flu shot application.8NPR. FDA Commissioner Makary Resigns The breaking point, according to a federal health official, was flavored e-cigarettes. Makary reportedly told associates he could not “in good conscience” authorize fruit-flavored vaping products marketed to young people, and had faced weeks of White House pressure to do so.9The New York Times. Trump Fires FDA Commissioner Makary
Kyle Diamantas, the deputy commissioner for food, is now acting commissioner. A senior administration official said the White House hoped to name a permanent nominee “in a matter of weeks,” but political observers expect Diamantas could serve in the acting role for an extended period given the approaching midterm elections.10Pharmacy Times. After Makary: What FDA Leadership Shake-Up Means for Pharmacy
The most consequential earlier departure was Dr. Peter Marks, who had led the FDA’s Center for Biologics Evaluation and Research since 2016 and played a central role in authorizing COVID-19 vaccines. Given the choice to resign or be fired, Marks resigned effective April 5, 2025. In his resignation letter he wrote that “truth and transparency are not desired by the Secretary, but rather he wishes subservient confirmation of his misinformation and lies,” and called the undermining of vaccine confidence “irresponsible, detrimental to public health, and a clear danger to our nation’s health, safety, and security.”11NBC News. FDA’s Top Vaccine Scientist Dr. Peter Marks Resigns An HHS spokesperson responded that Marks had “no place at FDA under the strong leadership of Secretary Kennedy.” Patrizia Cavazzoni, head of the FDA’s drug evaluation unit, had already left about two months earlier.12Reuters. Biotech Stocks Tumble on Reports FDA’s Top Vaccine Regulator to Leave
What Has Changed for Vaccines
Vaccine policy is the area where Kennedy has moved fastest, and where the courts have pushed back hardest. In June 2025, he fired all 17 members of the CDC’s Advisory Committee on Immunization Practices and replaced them with a new group that included several vaccine skeptics. In January 2026, he ordered an end to broad recommendations for universal childhood vaccination against influenza, rotavirus, hepatitis A, hepatitis B, certain forms of meningitis, and RSV, reducing routine recommendations from 17 to 11 vaccinations. The reconstituted ACIP also recommended against universal hepatitis B vaccination for newborns.13PBS NewsHour. Judge Blocks RFK Jr. From Scaling Back Childhood Vaccine Recommendations
Those changes are currently on hold. In July 2025 the American Academy of Pediatrics, the Infectious Diseases Society of America, the American College of Physicians, and other medical groups sued in federal court in Massachusetts, alleging violations of the Administrative Procedure Act and the Federal Advisory Committee Act.14Georgetown Law Litigation Tracker. American Academy of Pediatrics et al. v. Kennedy et al. On March 16, 2026, Judge Brian E. Murphy issued a preliminary injunction, ruling that Kennedy’s actions were “arbitrary and capricious” and that the government had “disregarded” established scientific methods. The order stayed the January 2026 schedule changes, blocked the appointment of 13 new ACIP members, and invalidated votes taken by the reconstituted committee. HHS said it would appeal.15NPR. Judge Blocks RFK Jr. Vaccine Changes The case remains active, with a joint status report due June 24, 2026.
What It Means for Drug Approvals
The first hard numbers on drug review performance came in the fall of 2025. An RBC Capital Markets analysis published in October 2025 found the FDA’s drug approval rate had fallen to 73 percent in the third quarter, down from a six-quarter average of 87 percent. Missed Prescription Drug User Fee Act deadlines rose to 11 percent from a historical average of 4 percent, and application rejections climbed to 15 percent from a historical average of 10 percent. Facility and manufacturing issues accounted for about 40 percent of rejections in 2025, up from 29 percent the year before.16Becker’s Hospital Review. FDA Drug Delays Rise in Q3
A separate January 2026 analysis from Endpoints News offered a more reassuring read, concluding that new drug review timelines had “mostly” not been affected and that FDA drug reviewers had been able to “hold the line” and meet nearly all performance goals despite staffing losses.17Endpoints News. FDA Staff Cuts Mostly Didn’t Impact New Drug Review Timelines, Analysis Finds The gap between the two pictures likely reflects the fact that the administration’s claim to have exempted reviewers from the cuts was at least partially true, even as the support functions around them were gutted.
What It Means for Food Safety
The food side of the agency has been less resilient than the drug side. Experts told Food Navigator USA in early 2026 that the loss of nearly 4,000 staff had forced the agency into “triage” mode, prioritizing short-term emergencies at the expense of long-term planning and preventive work. Inspection frequency was expected to decrease, with longer intervals between facility visits, and the agency temporarily suspended some food safety quality checks due to reduced laboratory capacity. Outbreak response was expected to slow because traceback investigations and coordination with the CDC and state agencies depend on institutional knowledge that walked out with experienced staff. Training a new inspector takes two to three years, so the lost capacity cannot be quickly rebuilt.6Food Navigator USA. FDA and USDA Staff Cuts Under Trump Raise Food Safety Risks
The early warning about food capacity came from inside the agency. Jim Jones, the FDA’s deputy commissioner for human foods and a former longtime EPA official brought in to reform the food division after the infant formula crisis, resigned on February 17, 2025. He said the firing of 89 staffers in his program, including ten people responsible for reviewing potentially unsafe food ingredients, made it “fruitless” for him to continue, and pointed to the administration’s “disdain for the very people” needed to improve food safety.18Food Safety Magazine. FDA Leader Jim Jones Resigns After Indiscriminate Firings in Human Foods Program
Other Policy Shifts You May Encounter
Beyond staffing and vaccines, the Kennedy-era FDA has moved on several fronts that touch specific products and industries:
- Food additives: On March 10, 2025, Kennedy directed a revision of the Generally Recognized as Safe (GRAS) rule, aimed at reviewing food ingredients on the market and removing many from the food supply. The agency launched a public Chemical Contaminants Transparency Tool on March 20, 2025.19FDA. Review of the President’s FY 2026 Budget Request for FDA – Senate Testimony
- Infant formula: “Operation Stork Speed,” announced March 18, 2025, mandates increased heavy metal testing, targets ingredient and labeling standards, allows more personal importation of foreign formula, and promotes U.S.-based manufacturing.5BioPharma Dive. HHS FDA Restructuring Layoffs Tracker
- Mifepristone: Kennedy tasked Makary with a “complete review” of the abortion pill’s labeling and its Risk Evaluation and Mitigation Strategy program.5BioPharma Dive. HHS FDA Restructuring Layoffs Tracker
- Drug advertising: Following a September 2025 executive order from President Trump, the FDA sent thousands of letters to drugmakers demanding compliance with advertising rules and issued roughly 100 cease-and-desist letters, with plans to use AI-powered tools to monitor prescription drug ads.5BioPharma Dive. HHS FDA Restructuring Layoffs Tracker
- Peptides: The FDA’s Pharmacy Compounding Advisory Committee is scheduled to meet in July 2026 to consider easing restrictions on seven peptides, including BPC-157 and TB-500, that were banned in 2023. Kennedy has publicly called the ban “illegal” and described himself as a “big fan” of peptides. The committee currently has three voting members and six vacancies.20The Guardian. FDA Peptide Restrictions
- Rulemaking process: Kennedy revoked the “Richardson Waiver,” signaling a shift away from traditional notice-and-comment rulemaking, and centralized most FDA policy and communications functions under HHS.5BioPharma Dive. HHS FDA Restructuring Layoffs Tracker
Where the Legal Fights Stand
Two lawsuits currently shape what the FDA is and is not allowed to do. The staffing case, brought by 19 states and the District of Columbia, produced the district-court injunction that the Supreme Court lifted on July 8, 2025, allowing the reduction in force to proceed. A related case, New York v. Kennedy, kept a temporary restraining order in place that protected certain employees at the CDC, the FDA’s Center for Tobacco Products, and a handful of other offices from the July terminations.7Fierce Biotech. HHS Terminates Employees After Supreme Court Allows Reduction in Force to Proceed The vaccine case, brought by the American Academy of Pediatrics and other medical groups, has already produced an injunction blocking the January 2026 childhood schedule changes and the reconstituted ACIP’s votes, with the appeal and further proceedings still pending.15NPR. Judge Blocks RFK Jr. Vaccine Changes
The FDA continues to carry out its core regulatory functions, approving new drugs, clearing medical devices, and authorizing tobacco products. It is doing so with roughly 16,600 employees instead of 19,000, no permanent commissioner, and an unusually large share of its rulemaking playing out in federal court. Whether the smaller, restructured agency can catch the next food contamination or drug safety problem before it reaches the public is, by its nature, a question that will only be answered after the fact.