Inside the FDA: Inheriting turmoil, new commissioner addresses morale, faces important tests, and says there will be no reorganization at the agency.

Weeks into his tenure, FDA Commissioner Dr. Marty Makary addresses turbulence described by current and former officials, asserts his independence, and holds hopes for a better agency.

Foreword: After preparing most of this piece, which relays discontent and concerns from some FDA employees, I reached out to FDA Commissioner Dr. Marty Makary for comment. He graciously agreed to an exclusive interview, which was co-published on Inside Medicine and MedPage Today earlier. Some of Dr. Makary’s responses are interwoven below, but the full Q&A offers additional insight and rare access to the views of the man now leading the FDA, so I encourage you to take a look at that, if you have not already.

Together, these two pieces provide the most complete picture yet of both the agency’s challenges and its new leadership’s approach.

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FDA Commissioner Dr. Marty Makary, with HHS Secretary Robert F. Kennedy Jr. looking on. Getty Images / Oliver Contreras

Some possible good news last week: The Associated Press reported that the FDA is moving forward with granting full approval to Novavax’s Covid-19 vaccine. Many observers welcomed the development after an unexpected recent delay in the process. The hiccup had cast doubts on the agency’s credibility and its ability to fulfill its regulatory functions independently under HHS Secretary Robert F. Kennedy Jr., whose statements have unfortunately undermined vaccine safety and effectiveness. Then, on Friday, the Wall Street Journal reported yet another wrinkle—that the FDA has apparently moved the goalposts on its decision by asking Novavax to conduct another clinical trial—leaving experts wondering if longstanding FDA standards had changed overnight.

Several current and former FDA employees who spoke to Inside Medicine on the condition of anonymity have come to see the Novavax story as a major test, not of Secretary Kennedy, but of their new commissioner, Dr. Marty Makary (who preceded me as editor-in-chief of MedPage Today), and the agency’s ability to function normally and independently. The sources described low morale in the wake of mass terminations by DOGE, and believe the cuts have harmed the agency’s ability to carry out the work of the American people.

Wary of RFK Jr., a circumspect FDA staff skips the honeymoon phase.

In the days after Commissioner Makary’s swearing in, one former FDA official told me that despite rumblings of misgivings in the rank-and-file at the agency, he still had a chance to succeed in the role, including in wonky but important areas where previous leaders had faltered. But within a few days of his tenure, many FDA employees were worried that Makary might be, in the words of one scientist, a “puppet commissioner.”

In fairness, given the agency's battered morale, even a flawless start would have been difficult for any new FDA leader in this moment, especially with RFK Jr. running HHS. But insider concerns were apparently augmented when Makary appeared at an FDA town hall earlier this month alongside his boss. During that town hall meeting, RFK Jr. accused the FDA of having become a “sock puppet” to industry, referred to Deep State conspiracy theories, and was misunderstood as having called young people with intellectual disabilities “retarded” (he was referring to the name of an old facility that his family had supported).

Many FDA employees walked out in the middle of these remarks, I was told. Dr. Makary has denied this, but at least one of my sources couldn’t answer a question about RFK’s remarks related to intellectually disabled people because she herself had already walked out. (My guess is that perhaps nobody walked out of the physical room where the main event was held, but some who attended simulcasts in large shared meeting spaces at the FDA did in fact bolt.) While the FDA rank-and-file have tended to show forbearance—and therefore do not directly blame Dr. Makary for RFK Jr.’s words—many were left with the impression that their agency boss inhabits a compromised position. Some feel that he is either complicit to or powerless to contradict RFK Jr.’s rhetoric, which one FDA scientist described using a word I won’t repeat here—but was, let us say, spicy.

For his part, Makary defended some of Secretary Kennedy’s remarks, specifically the sock puppet comment, saying his boss was referring to the past, not the present. Makary raised the example of OxyContin gaining FDA approval in 1995 based on a 14-day study. “In my view, that was industry capture, where there was undue influence.”

Novavax as a proving ground.

For some FDA employees and outside observers, the Novavax story is being watched as something of a canary in the coal mine for the issues that matter most to them. “If he bows to pressure, it could be something that he would never come back from,” the former FDA official said.

In our exchanges, however, it appeared to me that the Novavax question is less about pressure from Secretary Kennedy than about Makary’s own views on the FDA’s regulatory standards. Makary confirmed to me what the Wall Street Journal reported last week—that before the FDA grants full approval, he’d like Novavax to run a new clinical trial showing that its Covid-19 vaccine remains effective. (Shortly after we spoke, he tweeted a similar sentiment.) “Today, there is broad population immunity,” he said, “and the big question is does it provide a benefit?”

The issue, he argues, is that the Novavax Covid-19 vaccine was studied with immune-naive volunteers—that is, people who had never been infected or vaccinated. The same is true of Pfizer and Moderna’s fully approved mRNA vaccines, I pointed out. Makary’s response was that the FDA should return to “gold standard” science. He also said that he believes a successful trial today might increase uptake—not an argument we’d expect to hear from this administration, but an important one to consider. “[If] we had a study that showed that it helps today, it could significantly help improve the low Covid vaccine uptake we’ve seen.”

There are two problems here. First, as some have pointed out, if the FDA’s regulatory standards have suddenly changed, industry and the public need notification and a specific readout describing any changes. This can’t just happen on a whim. Second, even the appearance of an anti-vaccine stance while having RFK Jr. as a boss is fraught. This is neither Makary’s fault, nor can the landscape be entirely overlooked.

In my personal experience with Marty, I have not found him to be some closeted anti-vaxxer. However, in his interview (at 10:23 in the link) with CNN’s Dana Bash, he could not quite explicitly answer a general question—and a softball, at that—on whether Americans should be vaccinated, opting instead to say that he believes in vaccines, that it’s a tragedy when a child dies from a vaccine-preventable disease, and that he believes in the MMR vaccine. Still, the wordsmithing was hard to ignore. On this issue, he’s in a tough spot, I imagine. Throw his boss under the bus and risk losing his job—or speak narrowly and stick around to do the work he believes in? I tend to assume it’s the latter. (Dr. Makary addressed some of those goals in our interview.)

Addressing the RIFs rift, and more.

Other major issues have cropped up at the FDA since President Trump took office on January 20, leaving the rank-and-file dazed and confused, if not, at times, angry and demoralized. Generally, as I’ve written here, FDA employees have felt disrespected (the chaotic return-to-office ordeal, the infuriating “five-bullet email” debacle) or, worse, unsupported (the sudden loss of colleagues and important institutional resources) by this administration, all of which were initiated prior to Makary’s arrival. One current FDA scientist summarized the mood as “not great.”

Above all, many FDA employees feel that the reductions-in-force terminations (RIFs) at the hands of DOGE were unnecessary, cruel, and harmful to the agency’s effectiveness. In the fallout, a factual argument has emerged over whether any FDA scientists were fired when thousands of HHS employees were terminated by the Trump administration on April 1. While, again, Dr. Makary had nothing to do with this (the RIF plans were developed and implemented by DOGE before he was sworn in and, like all nominees to Senate-confirmed positions, he was not permitted to be involved), he did inherit the agency within days of the RIFs. And, since then, he has joined the chorus of administration supporters and insiders claiming that no scientists or researchers were axed in the RIFs. In fact, Dr. Makary repeated this on CNN last week and in our interview. However, The New York Times has reported that the FDA had to rehire some scientists in the agency’s food safety lab, which would tend to go against the claim. When we spoke over the weekend, Dr. Makary, seemingly for the first time, acknowledged that some of the RIFs may have had unintended effects that he wants to address, telling me, “If my center heads say they are running thin here or there, we take care of it. We’ve made some progress, like getting the library resources back up and running.”

Yesterday, after the Q&A was published, several FDA employees reached out to say that the library was still an issue. One source shared a screenshot indicating that access to UpToDate, an important online resource, was set to expire tomorrow. But later in the day, the source circled back saying that the expiration date had since been updated to July. (Some staffers still see the April 30 deadline on their screens.) Another pointed out that while specific library resources were touch-and-go, the librarians themselves are still gone, implying a worry that similar issues might become routine.

Still, Commissioner Makary’s acknowledgement that there are indeed fresh problems to solve related to the RIFs may be welcome candor to the FDA staffers I spoke to last week. For example, one source I spoke to (before my interview) said, “even though Makary keeps repeating the party line that RIFs didn’t affect scientific review staff, he’s ignoring the hemorrhaging of experienced reviewers and staff who are voluntarily leaving—early retirement or because of the oppressive and inhospitable environment.”

“Review staff [are] starting to resign, which is not a surprise but still sad,” another FDA employee told me. All told, terminated employees or resignations included pharmacology reviewers, toxicology reviewers, physicians, and regulatory project managers, the sources said. These losses occurred across multiple offices and divisions, reducing the effectiveness of the agency, I was told. In addition, library access to key resources remained a problem as recently as last week, some sources said. As a result, “we will absolutely be missing timelines, not for the most important things, but work is already being prioritized/de-prioritized,” one said. (Makary said that the library issues are being addressed, and, as above, there were signs of at least some progress.)

Dr. Scott Gottlieb, a former FDA commissioner during the first Trump administration, told CNBC last week that the agency’s ability to do its work has been compromised. He said that many FDA employees, seeing the writing on the wall and seeking private sector employment, have recused themselves from their typical activities, in accordance with ethics rules. (Gottlieb also pointed out that Trump administration cuts had slowed or halted work on generic drug approval.) In another example, Axios reported that a key drug database listing newly approved drugs (and changes to the labels of previously approved ones) had not been updated. It looks to me as though the FDA updated the list the next day, though, it’s unclear whether the update was just an administrative catch-up from that stemmed from RIFs, or whether journalistic pressure had made the difference.

Not a normal time. Can things go up from here?

What is clear is that things at the FDA are not normal. In our conversation, Commissioner Makary indicated an awareness of this—which, until now, seems to have been downplayed in previous public statements.

In my view, the FDA rank-and-file needs to hear this from him if morale is to improve and if the attrition of more good scientists is to be avoided. Addressing this head on can’t happen soon enough, it seems, and I believe an emerging sensitivity to rank-and-file morale at the FDA is at least part of the reason Marty granted me the interview. Indeed, the staffers I spoke with are not yet convinced that the new leadership has their back. “The silence from the commissioner other than silly MAHA stuff is deafening,” one of the scientists told me. “It’s the complete opposite of how to be an effective leader. Motivation and morale are through the floor.”

That said, it’s important to acknowledge that changes to longstanding practices (and the loss of friends and colleagues to sudden unexplained terminations) would be met with skepticism by the rank-and-file, regardless of the wisdom of the moves. And, as Makary said in our interview, it’s not like things were perfect before (though the current mood does seem substantially worse than it was.)

One piece of good news from our interview is that that widespread fears of a major reorganization at the FDA (read: more massive cuts)—like those being considered at other HHS agencies—appear to have been unfounded. Makary told me, for the first time publicly, that no major reorganization at the FDA is being considered, whether developed internally or by DOGE.

Moreover, former FDA officials from both Democrat and Republican eras have told me that there are important improvements to be made at the agency, and many still believe Makary retains the ability and opportunity to succeed in that. It’s just that, so far, there have not been examples of it happening, in part because of the turmoil he inherited. (The widely touted ban of certain food dyes has not yet occurred, nor would it likely make much or any difference, especially compared to other more serious problems we face.)

In sum, then, during the present administration, the FDA has lost many productive employees (leading to descriptions of decreased efficiency) and it may still lose more over diminished good will, eroded work conditions, and flagging confidence. “Maybe it’s all uphill from here,” I offered hopefully to one of the FDA employees I spoke to on Friday.

While she had not yet read my interview with Dr. Makary, her response indicated a steep climb: “😂”.

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If you have information about any of the unfolding stories we are following, please email me or find me on Signal at InsideMedicine.88.

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