Kennedy defended the decision, claiming it would bolster public confidence, insisting the move was “not about pushing any specific pro- or anti-vaccine agenda.” Rather, he said, it was meant to “prioritize the restoration of public trust.”

Criticism from the scientific community

However, experts quickly condemned the overhaul. Jesse Goodman, a former FDA Chief Scientist, called it “a tragedy,” warning that political interference in such expert bodies “will reduce confidence rather than increase it.” The ACIP, though advisory, plays a critical role in shaping CDC recommendations that affect vaccine accessibility and insurance coverage.

The Pharmaceutical Research and Manufacturers of America (PhRMA) echoed concerns, stating that dismantling ACIP injects uncertainty into public health policy and fuels vaccine skepticism. Shares of vaccine producers Moderna and BioNTech dropped over 1% in after-hours trading; Pfizer declined slightly.

Conflicts of interest allegations

Kennedy has alleged that the panel was riddled with conflicts of interest, charging that members routinely received funding from drug companies. However, no specific evidence was presented. Members are required to disclose any business or professional affiliations, and existing records show only minor recusals tied to clinical trial work.

The administration has yet to substantiate the claim that ACIP never rejected a vaccine - especially since the panel does not approve vaccines but instead advises on their deployment after FDA authorization.

All the current ACIP members were appointed during President Biden’s term, including 13 in 2024. Their dismissal allows the Trump administration, reinstated after the 2024 election, to shape the panel well before 2028.

“This is not a political committee, it’s never been partisan,” said Dorit Reiss, a legal scholar specializing in vaccine policy. She emphasized that historically, ACIP membership had remained untouched by direct presidential involvement.

The upcoming ACIP meeting is scheduled for June 25–27 at CDC headquarters in Atlanta. Experts are skeptical that a fully operational new panel can be seated by then, unless the administration has been quietly vetting candidates for some time.

Ongoing vaccine policy shifts

Kennedy’s approach to vaccine policy has already unsettled health officials. His tepid endorsement of measles vaccination amid a deadly outbreak has drawn sharp rebuke. Recently, he bypassed standard procedures to rescind the government’s recommendation for COVID-19 vaccination for healthy children and pregnant women.

Senator Bill Cassidy, a physician and Republican who had helped shepherd Kennedy’s confirmation despite past misgivings, voiced concern. “Of course, now the fear is that the ACIP will be filled up with people who know nothing about vaccines except suspicion,” he said on X, after speaking directly with Kennedy.

With the traditional ACIP role encompassing critical decisions about vaccine rollout and insurance coverage under laws like the Affordable Care Act, the stakes are high. The coming weeks will reveal whether Kennedy’s dramatic reshuffling deepens skepticism or, as he claims, begins to rebuild public faith.

This signals trouble for big pharma

Kennedy's latest move comes after Peter Marks’ quiet resignation in April from the FDA’s Center for Biologics Evaluation and Research. A key architect of Operation Warp Speed during Covid, Marks had long been seen as a steady, science-first voice inside the agency. 

In his resignation letter, Marks accused Kennedy of seeking not truth, but “subservient confirmation of his misinformation and lies.” For big pharma, this moment is a reckoning. Investors are taking note. Biotech stocks have dipped. Analysts at Cantor Fitzgerald have warned that Kennedy is dragging the country into “dangerous territory.”

In addition, the U.S. pharmaceutical industry is facing mounting uncertainty under Trump’s renewed policy stance, which includes potential tariffs, budget cuts at the Department of Health and Human Services (HHS), and an emphasis on lowering drug prices.

According to ING, these policies may inflict on pharmaceutical innovation. A proposed $33 billion (26%) budget cut to HHS, including the National Institutes of Health (NIH), threatens to shrink the pipeline for foundational, non-commercial research, further weakening the U.S.’s global leadership in drug development.

This financial and regulatory uncertainty may push companies to curtail R&D investment, especially as rising costs cannot be fully passed onto consumers. Reduced innovation could eventually benefit international rivals, notably China, whose contribution to the global drug pipeline has surged from 4% in 2014 to 27% in 2024.

Major U.S. pharmaceutical stocks have already taken a hit since the start of Trump’s second term, and investors should stay cautious about what lies ahead.