Marty Makary resigned as Commissioner of the Food and Drug Administration on Tuesday, ending a 13-month tenure that saw the agency buckle under the weight of a dual mandate that was never going to work. While President Trump publicly called him a "terrific guy" with a "great career in medicine" ahead of him, the exit was anything but voluntary. Makary was caught in a lethal pincer movement between Robert F. Kennedy Jr.’s skepticism and the administration's aggressive push for deregulation, specifically a high-stakes standoff over the approval of flavored e-cigarettes.
The departure of a commissioner after just over a year signals a deeper rot in the federal health bureaucracy. Makary was tasked with "making America healthy again" while simultaneously hacking away at the very regulatory structures that ensure drug and food safety. You cannot dismantle the fire department while asking it to put out more fires. By the time Makary submitted his resignation via text message—a screenshot of which was posted to Truth Social—he had lost the support of the White House, the confidence of his rank-and-file scientists, and the patience of the powerful lobbies he was supposed to court.
The Vaping Crisis and the Breaking Point
The immediate catalyst for the collapse was a fruit-flavored vape. For months, Makary had been quietly blocking the approval of flavored e-cigarettes, siding with traditional public health concerns over the risks to minors. This stance put him on a direct collision course with a vaping industry that had spent millions to convince the administration that flavors were the only way to migrate adults away from combustible tobacco.
Last week, the tension boiled over. Sources within the administration confirm that the White House applied immense pressure on Makary to reverse his stance. When the FDA abruptly authorized several fruit-flavored products from Glas Inc. on May 6, it looked like a victory for the industry. In reality, it was Makary’s surrender. By overriding his own scientists to satisfy a political directive, he destroyed his remaining credibility within the agency. Once the approval was granted, he was no longer useful to the political operatives who demanded it.
Institutional Memory in Freefall
The FDA is not just a building; it is a repository of decades of scientific expertise. Under Makary, that repository was systematically emptied.
Veteran regulators describe a culture of "endless self-promotion" and "micromanaging" that bypassed established scientific review processes. The numbers are staggering. Since early 2025, nearly 90% of senior leadership has left the agency. This includes the legendary Dr. Rick Pazdur, who retired after only three weeks of working under Makary, citing a "breached wall" between the commissioner’s office and the independent review staff.
When you lose people like Pazdur, you lose the ability to navigate complex clinical trial data. The results were immediate and messy:
- The Moderna Stand-off: The agency initially refused to review Moderna’s mRNA-based flu vaccine, only to be forced into a humiliating reversal after the company threatened a formal challenge and appealed directly to the White House.
- The Priority Voucher Scandal: Makary introduced the Commissioner’s National Priority Voucher (CNPV), a program designed to fast-track hand-selected therapies. Legal experts have flagged the program as potentially unlawful, as it bypasses federal rulemaking.
- Leadership Churn: The Center for Drug Evaluation and Research (CDER), the agency’s most critical arm, saw six different directors in a single year.
The Mifepristone Trap
While the vaping dispute was the final blow, the "slow-walking" of a review into the abortion pill mifepristone ensured Makary had no allies left on the right. Conservative groups, led by Susan B. Anthony Pro-Life America, had expected Makary to use his authority to severely restrict or remove the drug from the market.
Instead, Makary found himself stuck. On one side, he faced demands for an immediate, data-driven ban. On the other, he was dealing with a legal and scientific framework that made a summary removal nearly impossible without inviting a catastrophic defeat in court. By attempting to take a middle path—conducting a protracted review of "real-world evidence"—he ended up being viewed as a traitor by the pro-life movement and a radical by the left. Senator Josh Hawley’s celebration of the resignation as "welcome news" proves that in the current political climate, caution is often mistaken for incompetence.
The Kennedy Shadow
We must also look at the role of Health and Human Services Secretary Robert F. Kennedy Jr. It is now clear that Kennedy was the one who ultimately called for Makary’s head.
The two men were supposed to be ideological partners in the MAHA (Make America Healthy Again) movement, but their visions for the FDA were fundamentally incompatible. Kennedy wanted an agency that aggressively scrutinized the "toxic" influences of Big Pharma and Big Food. Makary, meanwhile, was focused on "reducing drug review times from a year to 1-2 months."
You cannot perform a deep-dive safety audit of the American food supply while simultaneously cutting the staff and the time required to do the work. Makary’s attempt to use "plausible mechanism" pathways for rare disease drugs—essentially approving drugs based on how they should work rather than how they do work—was a bridge too far even for some of his supporters. It created what analysts called "predictable volatility," a polite term for a regulatory environment where nobody knows what the rules are from one day to the next.
What Happens When the Guardrails Are Gone
Kyle Diamantas, the deputy commissioner for food, now takes the helm as acting commissioner. Diamantas is an attorney with close ties to Donald Trump Jr. and a background that leans more toward litigation than laboratory science. His appointment suggests the administration is doubling down on a loyalist-first approach to regulation.
The FDA currently has no permanent leadership in its top drug development departments. It is operating on a skeleton crew of acting officials. This matters because the agency is about to enter high-stakes negotiations for the reauthorization of user fee agreements—the multi-billion dollar deals with industry that actually fund the FDA’s operations. Without a confirmed, respected commissioner, the agency has no leverage.
Marty Makary came to Washington to "tell the truth" about American health. He leaves behind an agency that is faster, certainly, but also fractured, understaffed, and deeply distrusted by its own employees. The "difficulty" President Trump alluded to wasn't a lack of talent or hard work. It was the impossible task of trying to run an agency while the very people who hired you were actively dismantling the floor beneath your feet.
The FDA is now a ship without a rudder, headed into the most significant legislative negotiation in its history.
