FDA alleges fluoride supplements cause gut harms. Scientists aren't convinced

Under the leadership of Health Secretary Robert F. Kennedy Jr., the Food and Drug Administration is seeking to remove prescription fluoride supplements for kids from the market.

These are fluoride tablets, drops or lozenges that are recommended for kids who don't get fluoridated water to help prevent cavities.

The May 13 announcement from FDA claimed that ingested fluoride changes the human microbiome in a concerning way. "We're learning more about fluoride. It is damaging the microbiome," said FDA commissioner Dr. Marty Makary, in a May 16 episode of FDA Direct Podcast.

But other scientists point out that the research cited by FDA is inconclusive.

Makary also cast doubt on the usefulness of fluoride, citing a 2024 Cochrane review on the topic that says that "there is no evidence that fluoride actually reduces cavities in permanent teeth," Makary said on the podcast. In fact, the reviewers concluded that water fluoridation may slightly reduce tooth decay in children. He added: "It's debatable."

The move to pull fluoride supplements from the market contradicts years of research and best practices established by professional medical groups.

According to the announcement, the FDA plans to conduct a safety review and to take "appropriate action" to remove these products from the market by October 31. HHS also plans to issue "best practices for dental hygiene in children that are feasible, effective and do not alter gut health."

Unsubstantiated gut harm claims

The FDA announcement claims: "Ingested fluoride has been shown to alter the gut microbiome, which is of magnified concern given the early development of the gut microbiome in childhood," citing two literature reviews that explore the relationship between fluoride and the microbiome.

While the reviews find it likely that exposure to fluoride impacts the microbiome, both find that the effect is uncertain and may even be positive at low doses.

"I'm always pleasantly surprised when our research leaves the lab and does something," says Caroline Orr, a microbiologist at Teesside University in the UK, whose March paper in Nutrition Reviews was cited by FDA.

"But the studies that have been done show that, at low levels – the kind of concentrations that you'd see in water fluoridation or from brushing your teeth and spitting the toothpaste back out – [fluoride] doesn't impact the gut microbiome or the microbial community at all," she says. "If anything, some of the studies have shown that really small levels of fluoride might have a beneficial impact."

Orr's paper analyzed the currently available research on fluoride and the microbiome. She says there's not much, though what's out there indicates that the dose matters. "From a microbiome perspective, if you expose your microbiome to any chemical in high enough doses, it's going to have a negative effect," she says, "It's just a matter of finding out what that correct dose is."

She added: "I would be concerned if it meant that people just saw this as 'fluoride is bad' and stopped using fluoride in a way that dentists and doctors know is beneficial."

Both papers cited by FDA conclude that the evidence is limited, and more studies are needed.

'This removes a choice' for medical providers

The move contradicts recommendations from the Centers for Disease Control and Prevention and U.S. Preventive Services Task Force, along with professional medical associations including the American Academy of Pediatrics, American Academy of Pediatric Dentistry and the American Dental Association.

All of them recommend low doses of fluoride supplements for a limited cohort – children who live in areas without fluoridated water. Additionally, the professional medical groups specify their use should be restricted to those at high risk of getting cavities. The fluoride drops and tablets can only be obtained through a prescription from a dentist or pediatrician.

"This removes a choice," says Dr. Paul Casamassimo, chief policy officer for the American Academy of Pediatric Dentistry, "[It would] ban a treatment that is in the best interest of a patient, as determined by a trained, licensed health professional."

Fluoride supplements are not recommended for most children because most U.S. communities provide fluoridated drinking water, according to the CDC.

However, Kennedy has directed the CDC to revise its recommendations for community water fluoridation, blaming the practice — and ingesting fluoride generally — for a range of health problems, even though harms have not been found at the recommended levels. Though high levels of fluoride can cause tooth mottling, or discoloration, and may be linked with lower IQ, low levels of fluoride are generally considered safe and key to preventing cavities.

This latest action, combined with a wave of moves by state legislatures to ban fluoride from water systems, "is very, very serious for oral health," Casamassimo says. "It removes one of the tools that we as clinicians can use to stem tooth decay."

It's as though there's a disease and there's a medicine available to stop it — but clinicians are not allowed to prescribe it, he says.

Losing access to fluoride in community water and supplements will most affect populations that have the fewest options, says Dr. Princeton Ly, a pediatrician at UCLA Health. "The people who are going to hurt are those who don't have easy access to a dentist, have different insurance issues, housing issues, economic issues that prevent them from getting regular dental care," he says.

Ly previously researched the use of fluoride supplements in Hawaii, the state with the lowest levels of community water fluoridation in the U.S. Removing access to fluoride supplementation "puts a lot more onus on parents who are already having a tough time — and the disadvantaged kids are going to have the worst of it," he says.

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