Five critical challenges awaiting Marty Makary

MARTY MAKARY has been confirmed by the Senate as the next commissioner of the FDA. But Makary will almost immediately face challenges that will make his tenure as commissioner especially difficult. Here, AgencyIQ identifies and explores five of the biggest hurdles the new commissioner will face.

By Alexander Gaffney, MS, RAC | Mar 27, 2025 5:43 PM EDT

The incoming commissioner will be piloting the FDA amid confused seas

Beginning with the host of deregulatory executive orders issued in the first days of President DONALD TRUMP’s second term, 2025 has seen the FDA, along with other federal agencies, facing abrupt staffing reductions, compressed return-to-office timelines, the prospect of shuttered regional offices, and the intense oversight and technologic probing of ELON MUSK and the Department of Governmental Efficiency. Now, the FDA is facing the prospect of losing nearly one in five staffers with a newly announced HHS shakeup.
As MARTY MAKARY prepares to sit behind the FDA commissioner’s desk for the first time, he will oversee an agency going through tumultuous changes. How will Makary, a novice to federal service and large-organization leadership, address changes underway and plan for those to come – all while juggling internal and external pressures? AgencyIQ has identified five key challenges that will test Makary during his tenure as commissioner.

Agency transformation

The FDA is in the midst of several operational overhauls. In late 2024, the agency reorganized the Office of the Commissioner, the Office of Regulatory Affairs, and its human foods program to address ongoing operational concerns about siloed expertise and a lack of unified oversight. While the reorganization became effective last October, an organizational chart alone does not a reorganization make. By the end of the Biden administration, the FDA was still working out new processes, procedures and priorities for its reorganized divisions.
Realizing the potential of changes already effected or underway will be a Day One challenge for Makary. As the head of the Office of the Commissioner, he will play a direct role in overseeing some parts of the reorganized FDA. In other areas, such as the new unified Human Food Program and the Office of Inspections and Investigations (OII, formerly ORA), Makary will have a vested interest in ensuring operational success if he wants to have more stringent oversight of the American food supply or medical products.
But that is not even close to the only operational transformation that Makary will face. The Trump administration has called for federal agencies to submit Agency Reduction-in-Force and Reorganization Plans to identify ways to reduce current staff and further reorganize agencies in a bid to make them smaller and more efficient. The process of deeply cutting staff and programs may well be hugely challenging for Makary, who is arriving at the FDA without the benefit of experience leading large organizations or a history of government service.
But even if Makary does have a knack for handling operational challenges, the prospect of thousands of FDA staff leaving the agency in the coming months – both through RIFs and voluntarily through retirements and attrition – will mean difficult choices about how to carry out the agency’s existing mission with fewer resources. On March 27, HHS announced that it plans to terminate approximately 3,500 FDA staff, largely from administrative, information technology, human resources, finance, communications and policy roles. These are the people who make it possible for other staff to do their jobs and generally ensure the day-to-day functioning of the FDA. Their absence is likely to mean some FDA operations will grind to a halt.
While HHS Secretary ROBERT F. KENNEDY JR. said the goal of the changes would be to make health care agencies more efficient, it seems just as likely that FDA will have less capacity and capabilities to accomplish some of its existing workload – mandated by statute and obligated by already-committed industry user fees — and will need to cease some activities.

The learning curve for Makary – and his leadership staff

Makary’s challenges in tackling significant agency transformations will be exacerbated by a brain drain of experienced staff. Since the start of the year, the FDA has seen the departure of its former Principal Deputy Commissioner NAMANDJE BUMPUS, Chief Counsel MARK RAZA, Chief of Staff ELIZABETH JUNGMAN, Deputy Commissioner for Policy, Legislation, and International Affairs KIMBERLEE TRZECIAK, Deputy Commissioner for Human Foods (JIM JONES), its Chief Operating Officer (JAMES SIGG), its Associate Commissioner for External Affairs LEAH HUNTER, and the Director of the Center for Drug Evaluation and Research,PATRIZIA CAVAZZONI.
So far, staff chosen for permanent replacements are generally inexperienced with the FDA or have never worked for the agency before, like newly appointed Chief of Staff JIM TRAFICANT, Chief Operating Officer BARCLAY BUTLER, and Deputy Commissioner for Human Foods KYLE DIAMANTAS.
For Makary himself, the FDA learning curve will be steep. The agency regulates a dizzying variety of products – drugs, medical devices, diagnostics, biologics, food, tobacco, cosmetics, veterinary products, radiological products and more – representing about a fifth of U.S. gross domestic product, according to a 2020 FDA estimate. Even for experts deeply versed in FDA regulation, the extraordinary array of products regulated by the agency can exceed the capacity of any single person to be conversant on every regulatory topic. Traditionally, that has meant that new commissioners lean heavily on existing and experienced staff to help them navigate emerging regulatory issues, crises or political problems. But for Makary, an absence of experienced FDA staff in the senior ranks, in combination with likely antipathy from FDA staff who have witnessed their colleagues’ terminations, may combine to make Makary’s learning curve especially difficult.

Finding the capacity to do what Makary wants

Every new FDA commissioner comes into office with a wish list of policies, programs and priorities they wish to pursue. Some are even lucky enough to accomplish them.
But for most commissioners, crises cut short their ambitions. Former commissioner STEPHEN HAHN dedicated nearly all of his tenure to handling the Covid-19 pandemic. ROBERT CALIFF spent much of his most recent stint at the agency reforming the agency, being blamed for FDA inaction on infant formula shortages, and tacking the opioid crisis. MARGARET HAMBURG spent considerable time and effort trying to resolve drug shortages and a series of political crises (including HHS overruling the agency’s approval of the OTC birth control medicine Plan B One Step).
The point being: It remains unclear which crises Makary will face, but it’s a near-certainty that he will be tested during his tenure. Those tests will raise a few key points for observers to monitor. First, how will Makary handle those crises? The FDA will have less funding, fewer staff and less political capital than it did under his predecessors, inherently making crisis response more challenging. Second, what priorities of Makary will fall victim to ensuing crises? People and institutions alike share capacity limits. While experience, redundancies and resources can help increase capacity, Makary’s administration will face relative shortages of all three, thanks to staff turnover and a greatly pruned budget and roster.
And then there are the political pressures Makary will face. Makary is not known as a thought leader on FDA regulatory policy topics. Trump did not select him for his extensive agency experience, regulatory record or platform of ideas. But there are plenty of politicians in the Republican party and in Trump’s orbit who do have strong opinions on specific FDA regulatory topics, and they are likely to put pressure on Makary to take action. For example, Makary is likely to be pressured to modify risk controls for the abortion drug mifepristone and to modify authorization conditions for Covid-19 vaccines. Makary is also likely to face pressure from his boss, HHS Secretary Kennedy, to take further action on other topics such as foods regulation, vaccine safety, and industry’s relationship with the FDA. Addressing these pressures, Makary’s actions – whatever they may be – will likely become a flashpoint, attracting negative public attention, political pushback, and even resignations of key agency leaders. These are all distractions that could diminish Makary’s capacity to accomplish his desired agenda.

What does Makary want to do?

Makary hasn’t yet said much about his desired goals for the FDA. During his confirmation hearings, Makary displayed a remarkable ability to stay on-message and not divulge much of substance on the regulatory agendas held by him, Kennedy, or Trump.
There were a host of major regulatory questions that we had hoped Makary might be asked as part of his confirmation process.
- These are among the questions we had:
  
  – What will Makary do about compounded drugs for GLP-1s, especially now that FDA has declared a shortage over the weight loss drugs and said that compounding must halt?
  
  – Given Makary’s past writing about Covid-19 vaccine boosters, will he order them to be taken off the market? Or advise restricting their administration to narrower groups?
  
  – What does Makary think about industry user fees? What approach will he take to upcoming negotiations between FDA and industry?
  
  – How will Makary work with Kennedy. – especially in light of the HHS Secretary’s skeptical views on vaccines?
  
  – Will Makary be active in medical product decisions, or will he leave them to FDA reviewers to make (as past commissioners have mostly done)?
  
  – Given the focus of the Make America Healthy Again (MAHA) movement that Kennedy’s affiliated with, how would Makary address issues of “industry influence” within the FDA?
  
  – Given this administration’s ongoing focus on agency efficiency, which parts of the FDA does Makary plan to reform or eliminate? What parts would he protect or reinforce?
  
  – What does Makary think about the removal of diversity, equity and inclusion documents at the FDA – and the retroactive scrubbing of certain associated terms from FDA webpages and guidance?
  
  – How will the deregulatory executive orders restrict Makary’s ability to advance his own agenda at the agency? How does he plan to work with the White House to advance regulatory policies that are critical to public health? Which types of regulations and guidance does he plan to eliminate as part of the 10-for-1 executive order?
  
  – Does Makary support existing regulations with upcoming implementation dates, such as the Laboratory Developed Test (LDT) final rule, the Additional Conditions of Nonprescription Use (ACNU) final rule, and the Drug Supply Chain Security Act’s (DSCSA) enhanced supply chain provisions?
  
  – Are there any specific regulations, guidance, policies or approved products that he would rescind?
  
  – How would Makary reform FDA’s advisory committees? Does he believe that they are imbued with too much industry influence?
In short order, Makary will need to answer many of these questions in both words and actions.

Dealing with the consequences

A classic responsibility of the FDA commissioner is to absorb and respond to criticism. And Makary is likely to be the recipient of an unusually large amount of criticism – even anger – from public stakeholders in the months ahead.
Any organization that loses a significant portion of staff to layoffs, retirements and attrition (not to mention likely budget cuts) will see a degraded level of service.
But the FDA isn’t just “any organization.” Its staff are reviewing life-saving and -sustaining products. Degradations in service can result in approval delays for these products. Laid-off policy staff can result in shrunken and stretched offices – and hence, inconsistent review decisions and wasted development resources. Fewer staff available to answer phones can result in desperate patients not getting access to emergency compassionate use trials.
Even when the FDA is fully staffed, it attracts scrutiny for problems, even those problems not fully within its control. Take drug shortages: The FDA can’t order manufacturers to continue to make drugs, it doesn’t regulate the production of chemicals ingredients, and it’s generally not in control of most of the drug supply chain. Nevertheless, Congress has consistently asked the FDA to take a more active role in mitigating drug shortages.
For Makary, many of the same issues that plagued his predecessors – drug shortages, a lack of inspections of foreign drug facilities, drug quality testing issues, challenges keeping up with technological advancements, and shortages of critical staff – are likely to recur during his tenure due to resource constraints or other political issues. It’s hard to tackle drug shortages if you have fewer staff with which to coordinate on drug shortages issues, for example.
This dynamic could mean that Makary spends a significant amount of his administration trying to re-solve issues that had been addressed (though not necessarily solved) by his predecessors and by Congress.

To contact the author of this piece, please email Alec Gaffney ( agaffney@agencyiq.com).
To contact the editor of this piece, please email Kari Oakes ( koakes@agencyiq.com).