Robert F. Kennedy Jr. (RFK Jr.) has been confirmed by the Senate as secretary of the Department of Health and Human Services (HHS). In this capacity, RFK Jr. will oversee 13 agencies that are critical to U.S. health policy, including the Food and Drug Administration (FDA), Centers for Medicare & Medicaid Services, Centers for Disease Control and Prevention (CDC), National Institutes of Health (NIH) and other health services.
RFK Jr.’s path to becoming HHS secretary began with his candidacy in the 2024 presidential election. As a presidential candidate (as well as prior to launching his campaign), Secretary Kennedy took numerous policy positions on health-related issues — largely focused on products under FDA’s jurisdiction — that may influence his priorities as HHS secretary.
This article considers what may be coming at federal health agencies, and particularly at FDA, based on Secretary Kennedy’s previously articulated policy positions as well as initiatives that the Trump administration has undertaken during the past month.1
Funding for Research and Staffing
The Trump administration has made downsizing the federal government a hallmark of its first month in office, and this approach is likely to impact FDA as well as other HHS agencies.2 Secretary Kennedy’s public remarks do not suggest he would oppose widespread staffing cuts at FDA, particularly if they reduce the agency’s reliance on user fees, which Secretary Kennedy views as a conflict of interest. (See our January 22, 2025, client alert “Gauging the Likelihood of Trump Administration FDA Reforms.”)
Separately, Secretary Kennedy has spoken publicly about redirecting funds from NIH research to what he has described as preventive, alternative and holistic approaches to health. He has also suggested he would like to downsize the staff at NIH.
- Cuts to NIH grantmaking. On February 7, 2025, NIH announced its intention to sharply reduce its funding of indirect costs incurred by grant recipients to 15%, down from previous levels of 50% or more. While a federal court has since issued a temporary restraining order blocking implementation of this measure, it is clear that changes to NIH funding and staffing are on the agenda for Secretary Kennedy and the Trump administration. If implemented, this is likely to impact both public and private sector research and development for new drugs, which often come out of partnerships with NIH, as well as clinical trials, which are often conducted at NIH-funded sites. Companies planning clinical studies that may involve NIH may wish to consider backup plans, and those that have existing or planned Cooperative Research and Development Agreements with NIH or other federal laboratories should review the terms of those agreements to ensure they are prepared for potential changes.
- Changes in user fee programs. As discussed in our prior article, while Secretary Kennedy has expressed skepticism about user fee programs, they are the bedrock of current FDA operations. Although the Trump administration could face challenges if it seeks to dismantle programs established by the current commitment letters (which have been ratified by Congress), most user fee programs are due for reauthorization in September 20273 and could be subject to opposition from the administration and its supporters in Congress. In the event of major staffing cuts at FDA, the first programs to be eliminated may be those established via commitment letters (rather than statute), which rely on user-fee-funded staff. More generally, if user fees are cut or eliminated, the result could be similar to a pre-1992 posture, before passage of the Prescription Drug User Fee Act (PDUFA), without clear review timelines and a much longer FDA review process. To avoid this scenario, former FDA Commissioner Scott Gottlieb has publicly suggested that FDA and industry encourage Congress to extend the term of the current user fee amendments rather than renegotiate with the current administration.
- Race to submit new products. Given the uncertainty surrounding user fee programs, we may see a crush of product applications submitted before the expiration of current user fee programs, including PDUFA VII and Medical Device User Fee Amendments V. Companies may feel particularly pressed to seek approval of innovative products that rely on pilot programs established via guidance or user fee commitment letters, such as the Real-Time Oncology Review and the Center for Devices and Radiological Health’s Total Product Life Cycle Advisory Program. If the new user fee programs are significantly minimized and FDA’s staffing is cut, this could significantly impact review timelines. Companies whose development plans hinge on programs authorized by user fees may wish to make backup plans in case products cannot be submitted prior to September 2027, or accelerate development timelines to submit prior to expiration of the current user fee programs.
- Fewer guidances and regulations. On January 31, 2025, President Donald Trump issued “Unleashing Prosperity Through Deregulation” (Executive Order 14192), which dictates that “whenever an executive department or agency (agency) publicly proposes for notice and comment or otherwise promulgates a new regulation, it shall identify at least 10 existing regulations to be repealed.” While a similar executive order was issued during the previous Trump administration, that called for repeal of fewer regulations and guidance, and FDA responded by unpublishing older guidance documents. This order could result in FDA publishing fewer guidance documents, particularly if it does not have sufficient wiggle room remaining to continue repealing guidance at a 10-for-1 pace. Fewer guidance documents could, in turn, impede development programs and lead to more Complete Response Letters or refusals to approve products.
Vaccines
Secretary Kennedy has been a longtime skeptic of vaccines and was a vocal opponent of state and federal COVID-19 vaccine mandates. After being nominated, Secretary Kennedy softened his position somewhat, stating that every American who wanted a vaccine for themselves or their children would have access to it if he became secretary.
He also reportedly made some concessions on vaccines in order to gain the vote of Sen. Bill Cassidy, R-La., to move through the confirmation process, committing to maintaining the CDC’s Advisory Committee on Immunization Practices (ACIP) recommendations without changes and allowing the CDC to keep statements on their website that vaccines do not cause autism.
At the same time, Secretary Kennedy declined to disavow his claim that vaccines are linked to autism during his confirmation hearing. And, as secretary, he will wield considerable power with respect to vaccines even if he does not oppose them.
- Public meetings and dockets. FDA holds public meetings and opens public dockets to solicit comments on a wide variety of topics. A public meeting on vaccines could increase public dialogue on the issues important to Secretary Kennedy, and a corresponding public docket could provide FDA with comments to consider in future guidance or rulemaking.
- Withdrawal of guidance documents. Since President Trump took office, information has been removed from various health agency websites in response to executive orders. FDA’s website currently includes almost 20 guidance documents that offer scientific advice on vaccine development, which industry relies on to support vaccine development programs. Withdrawing some or all of this guidance would leave industry without information needed to plan development programs.
- More stringent development and approval criteria. While the standard for approval of a new drug (including vaccines) is set by statute, FDA reviewers have significant scientific leeway when considering data submitted to support submission and approval of biologics license applications. Under more vaccine-skeptical HHS leadership, FDA could set more stringent requirements for vaccine study design, approval, chemistry manufacturing and controls without any rulemaking or guidance process.
- Staffing cuts. Many of the key staff involved in the approval of the COVID-19 vaccines left the Center for Biologics Evaluation and Research’s Office of Vaccines Research and Review (OVRR) prior to President Trump’s second inauguration. Any further downsizing in OVRR staff would likely slow the vaccine development, review and approval process.
Foods
A primary focus of Secretary Kennedy’s “Make America Healthy Again” agenda is improving nutrition in the United States. Secretary Kennedy has proposed a wide range of measures, including a revamp of the FDA office in charge of nutrition labeling, as well as more transparent labeling, increased FDA oversight over ultra-processed foods, removal of such foods from school lunches and bans on food additives and chemicals.
It is quite likely that we will see increased focus on food policy under Secretary Kennedy. Potential developments include:
- Nutrition labeling reform. At the end of the Biden administration, FDA introduced a proposed rule on front-of-pack nutrition labeling with the stated goal of helping consumers make healthier food choices. This rule seems likely to be finalized under Secretary Kennedy, perhaps with a shorter-than-usual implementation window for industry.
- Coordination with other agencies to limit consumption of ultra-processed foods. The Women, Infants and Children (WIC) program and Supplemental Nutrition Assistance Program (SNAP), both administered by the Department of Agriculture (USDA), provide access to food for people living under federal poverty limits. Only certain foods are eligible for purchase using WIC and SNAP assistance, and a coordinated effort between FDA and USDA — perhaps with nutritional standards attached — could limit the billions of federal dollars currently spent on ultra-processed foods under these programs.
- Revamping the Generally Recognized as Safe (GRAS) process. Secretary Kennedy has repeatedly stated that he would like to limit food additives and chemicals in ultra-processed food. As discussed in our prior article, many food additives, as well as new dietary ingredients used in dietary supplements, currently come to market through the GRAS process. Tightening the standards for GRAS and pushing more additives into the premarket review process would create more oversight for new food additives. We also may see FDA banning more food additives, as it did with Red Dye No. 3 at the end of the Biden administration.
- Creation of a single food safety agency. Currently, food safety is managed both by FDA and USDA’s Food Safety and Inspection Service (FSIS). During his first term, President Trump issued Executive Order 13781, which called for a single food safety agency that would consolidate both FDA and FSIS inspectorates. This reform has also been called for by food safety experts, and a consolidated organization would be consistent with the current administration’s staffing and efficiency goals. However, as we previously discussed, this reform would not be simple given FDA’s current statutory authority over food under the Federal Food, Drug, and Cosmetic Act.
- Increasing access to raw milk. Secretary Kennedy is a proponent of the purported health benefits of raw milk, which is unpasteurized and therefore does not meet FDA’s pasteurization standards. Currently, FDA exercises enforcement discretion over (i.e., chooses not to pursue) interstate commerce in raw milk, while states vary in their treatment of it. It is unlikely FDA would issue regulations allowing for interstate commerce in raw milk, but it could formalize its exercise of enforcement discretion through a published policy.
While it is difficult to predict which of Secretary Kennedy’s policy positions will ultimately result in real-life changes, it is clear that an uncertain time for FDA has begun. Anticipating potential challenges that may arise due to changes in policy will be critical for medical product developers and other FDA-regulated companies, as well as those that rely on funding and operations of other U.S. health agencies.
See the Executive Briefing publication
1 This note assumes that the next FDA commissioner will work to implement Secretary Kennedy’s policy positions; if this is not the case, change may not be as rapid or profound.
2 Press reports have suggested FDA staff may be cut by nearly half, with probationary staff or those with poor performance reviews being most affected. The impact of return-to-office policies on FDA also will be significant, as a large portion of agency staff continues to work remotely.
3 The over-the-counter monograph drug user fee program is due for reauthorization in September 2025.
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