RFK Jr. is confirmed as HHS secretary. What now?

The Senate voted 52-48 to confirm Robert F. Kennedy Jr. as the next secretary of the Department of Health and Human Services (HHS). Under Kennedy’s leadership, HHS and its agencies – including the FDA – will almost certainly implement significant policy shifts, as federal health agencies also steel for profound resource reductions.

Today, the Senate confirmed Robert F. Kennedy Jr. as HHS secretary in a 52-48 vote

• The vote followed party lines, with the exception of Rep. MITCH MCCONNELL (R-Ky.), who voted against the confirmation.
• This was the final step in the confirmation process. Just as for the FDA commissioner, the HHS secretary is appointed by the president and confirmed by the Senate. [ See AgencyIQ’s confirmation logistics explainer here.].

Kennedy’s road to confirmation offers insights into his vision for the department and its constituent agencies

• Leading up to the election, DONALD TRUMP discussed his plans to have ROBERT F. KENNEDY JR. lead his health policy portfolio [ Read AgencyIQ analysis here.]. Kennedy is known for his longtime opposition to the way FDA regulates vaccines, and his involvement with Children’s Health Defense group and the “ Make America Healthy Again” movement. In a post on the social media platform ‘X’ (formerly Twitter) on Oct. 25, 2024, Kennedy wrote: “FDA’s war on public health is about to end. This includes its aggressive suppression of psychedelics, peptides, stem cells, raw milk, hyperbaric therapies, chelating compounds, ivermectin, hydroxychloroquine, vitamins, clean foods, sunshine, exercise, nutraceuticals and anything else that advances human health and can’t be patented by Pharma. If you work for the FDA and are part of this corrupt system, I have two messages for you: 1. Preserve your records, and 2. Pack your bags.”
• On Nov. 14, 2024, Trump announced his intent to nominate Kennedy as his HHS secretary. The nomination was officially transmitted to the Senate on January 20, 2025. [ Read AgencyIQ’s analysis of the nomination here.].
• Kennedy advanced through late January hearings with the Senate’s Finance and Health, Education, Labor and Pensions (HELP) committees. The vetting process came with some friction by way of contentious interactions between Kennedy and HELP Chair Sen. BILL CASSIDY (R-La.) regarding vaccine safety. [ Read full AgencyIQ analysis on Kennedy’s vaccine policy levers here.]. Cassidy, a gastroenterologist, ultimately cast the deciding vote to advance Kennedy’s HHS secretary nomination to the full Senate. As reported by our POLITICO colleagues, Kennedy committed to have an “unprecedentedly close relationship” with Cassidy, with regular meetings.

The Senate has also compiled a record of Kennedy’s written responses to questions

• In addition to the live interactions that took place at these hearings, Kennedy submitted written responses to several hundred questions for the record. These are available in five parts from the Senate Finance Committee. The questions cover a broad range of topics, with the threads most germane to FDA and the products it regulates teased out below.
• FDA product review and capacity: In response to questions from Sen. TODD YOUNG (R-Ind.), Kennedy committed to “support FDA and its staff in the efficient review and approval of innovative new therapies” but fell short of committing not to cut FDA drug reviewers or funding. In response to a later question from Sen. ELIZABETH WARREN (D-Mass.), he explained, “I’m not going to make any staffing decisions before being sworn in as Secretary and investigating any issues.” When asked about the “gold standard” of scientific review for the FDA, Kennedy said, “I believe the staff at FDA are genuinely working to protect and promote the public health. But I also believe we need radical transparency to keep the trust of the American people.”
• Clinical trials: When asked about his concerns with the clinical trial process by Sen. Ron Wyden (D-Ore.), Kennedy responded, “Well-designed clinical trials are essential in determining the benefits and risks of new medical products. You can look to President Trump’s Operation Warp Speed, and the clinical trials it accelerated, for lessons in how to improve upon the clinical trial process generally. I support such rigorous study, and, if confirmed, will support efforts to make research faster, cheaper, safer, and more informative.”
• Drug patents: Kennedy received multiple questions related to FDA’s Orange Book, which lists drug patents and has been criticized for unreasonably extending exclusivity [ See AgencyIQ analysis here for additional background.]. In response to a question from Warren, he said, “I agree that FDA should promote prescription drug competition to bring down drug costs for the American public. For too long, the pharmaceutical industry has worked to game the system to delay generic and biosimilar competition. If confirmed, I commit that I will work with FDA staff and others to consider the specific approaches you have raised.”
• Mifepristone: Kennedy provided the same answer to multiple questions regarding his approach to regulation of medication abortion drug mifepristone, stating, “We need to understand the safety of every drug, including mifepristone. As I stated during the confirmation hearing, President Trump has made it clear that he wants HHS to study the safety of mifepristone to ensure patient safety.”
• Vaccines: Kennedy also used the same language to respond to numerous questions regarding vaccine policy, stating “If confirmed, I will do nothing as HHS secretary that makes it difficult or discourages people from taking vaccines but instead seek transparency in these products.” When asked whether he would interfere with or overrule FDA decisions regarding review or approval of vaccines, he said, “If confirmed, I will ensure a review of drugs for safety and efficacy in accordance with the law.” As AgencyIQ has previously discussed, all FDA actions are legally able to be reviewed, approved and even reversed by HHS leaders. This includes facets of vaccine regulation beyond product approvals and withdrawals, like product labeling, risk controls, guidance, and more.

Kennedy is set to lead a department in a crucible, as multiple government reform efforts converge

• On Feb. 13, just hours after Kennedy’s confirmation, Trump issued an Executive Order (EO) spelling out priorities for Kennedy: Make America Healthy Again (MAHA). The order establishes a federal MAHA commission to be chaired by Kennedy and staffed by several other federal leaders, including the FDA commissioner. The MAHA commission is directed to make several sweeping reforms to health care and research systems, including increasing transparency in federally funded research, finding root causes of childhood and chronic illnesses, and developing a strategy to “Make our Children Healthy Again,” to include investigations into existing drug products.
• Trump policy implementation: In addition to the MAHA EO, President Trump has signed more than 50 executive orders since his inauguration, many of which have major impacts on HHS and FDA [ See AgencyIQ’s analysis of what Trump’s executive orders mean for the FDA and the life sciences industry here.]. Importantly, this includes the new deregulatory EO that directs agencies to eliminate or rescind 10 “regulations” for every regulation issued – with “regulation” broadly defined. As AgencyIQ has previously discussed, this order is likely to significantly constrain policymaking across the department. During Kennedy’s late January nomination hearing before Senate Finance, Sen. BEN RAY LUJÁN (D-N.M.) asked him about FDA’s 2024 draft Diversity Action Plan (DAP) guidance, and he verbally committed to finalizing the document then. Since then, though, Trump has issued an executive order (EO) directing agencies to terminate their diversity-related “action plan” policies, which led to the DAP guidance being pulled from the web. The draft DAP guidance has been reinstated following a Feb. 11 temporary restraining order, but its future remains uncertain as litigation proceeds [ See AgencyIQ analysis here.].
• Workforce: As described above, Kennedy will oversee significant workforce changes at HHS, including FDA. A February 11, 2025 EO specifically calls for agencies to work with DOGE to reduce workforce size, stating that federal agencies will only be able to hire “one employee for every four employees that depart,” subject to some public safety exceptions. [ See AgencyIQ analysis of that order here.].
• Funding: Congress faces a March 14, 2025, deadline to pass a FY 2025 budget or another Continuing Resolution (CR). As reported by our POLITICO colleagues, a Republican-authored budget resolution is currently on deck for consideration by the House Budget Committee that proposes spending cuts across the board. The resolution text does not currently provide details on the budgets for HHS and FDA. As AgencyIQ has previously discussed, Trump’s DOGE-led push to slash staffing and nix large swaths of regulations could leave Kennedy stymied in his stated goals of achieving more stringent FDA safety review and monitoring, and ending industry funding for the FDA.
• More budget realities: Though Kennedy is about to take over an agency with an ambitious to-do list, he may well spend most of his time not being able to achieve much more than manage decline and extremely challenging political decisions. This will especially be the case if the Republican party cuts Medicaid to the extent that it likely will, under the House Budget Resolution package that is currently being negotiated.

What’s next?

• The main takeaway: Regulatory uncertainty is certain. Ongoing reform efforts leading to decreased FDA resources, coupled with a Kennedy agenda to heighten scrutiny of certain FDA-regulated products, result in a hazy picture of what the rest of 2025 — and the following years of the Trump administration — will look like for the life sciences industry.
• One area of particular uncertainty: User fees. The fees industry pays to FDA are a primary funding source for the agency. Across the board, at $3.5 billion, user fees account for just under half of the FDA’s FY2025 $7.2 billion budget proposal. As AgencyIQ has previously discussed, all user fee programs could be at some degree of risk during a Trump administration. Kennedy said in November 2024 that President Trump instructed him to root “the corruption and the conflicts out of the regulatory agencies” and to “return the agencies to the gold standard empirically based, evidence-based science and medicine that they were once famous for.”
• But there’s reason to think that Kennedy believes the agency’s user fee programs to be evidence of corruption and conflict. Children’s Health Defense, which Kennedy founded and where he served as board chair and chief litigation counsel, states on its website that “user fees introduce potential conflicts of interest into the FDA’s regulatory process.” The Prescription Drug User Fee Act (PDUFA) reauthorization process begins in July 2025, with a planned September 2025 kickoff meeting launching a negotiating process that typically lasts several months. This timing means that Kennedy has time to disrupt these negotiations, play hardball with industry, or even walk away from negotiations entirely, leaving the PDUFA program to collapse and end. [ For an explanation of how the PDUFA program will be reauthorized this next cycle, please read AgencyIQ’s analysis here.].
• Kennedy’s confirmation tees up hearings for the nominees to lead agencies within HHS. The process of installing leaders in these key positions may shed more light on the specific changes to expect. As of Feb. 12, a Senate HELP hearing had not been scheduled to consider MARTY MAKARY’s nomination for FDA commissioner [ Read AgencyIQ’s analysis of what to expect here]. The nominees to direct the National Institutes of Health (JAY BHATTACHARYA) and the Centers for Disease Control and Prevention (DAVE WELDON) remain in the same holding pattern.
• Look out for who Kennedy brings with him, too. Department secretaries play key roles in hiring other leadership staff, senior advisors, general counsel and more. These staff are the ones running the agency on a day-to-day basis and can exert extraordinary influence as they carry out the work of writing regulations, enacting policies, building out department-wide policy agendas, and generally driving change.

Featuring previous research by Alexander Gaffney and Laura DiAngelo.

To contact the author of this item, please email Amanda Conti ( aconti@agencyiq.com).
To contact the editor of this item, please email Kari Oakes ( koakes@agencyiq.com).

Key Documents and Dates

• PN11-8 — Robert F. Kennedy Jr. — Department of Health and Human Services