Robert F. Kennedy Jr.’s long history as a skeptic of vaccines has come full circle as his former nonprofit is suing the Centers for Disease Control and Prevention — which Mr. Kennedy now oversees in his capacity as President Trump’s health secretary — accusing it of forcing disadvantaged children to get Covid vaccinations.

The key plaintiff in the lawsuit is a California pediatrician who served disadvantaged families and is suing the CDC after her refusal to give Covid-19 shots to her patients “based on her professional judgement” cost her Medicaid patients and ultimately, she says, her medical practice.

Samara Cardenas, a doctor from Anaheim, claims that the CDC’s Vaccine for Children program, which provides vaccinations to Medicaid-eligible children, is forcing physicians like her to “administer the investigational COVID-19 vaccine, which has never been shown to confer any clinical benefit to healthy children, years after the pandemic ended, and when the risk to children had virtually disappeared,” according to the lawsuit. 

Dr. Cardenas’s attorney, Richard Jaffe, told the Sun the lawsuit, which is supported by Children’s Health Defense, a nonprofit formerly led by Mr. Kennedy that is known for its hard anti-vaccination positions, shines a light on what he sees as a larger problem of “when you leave public policy to people who have, I would consider, an overly narrow focus.”

Mr. Jaffe argues that the federal government’s insistence on “perpetuating this obsolete policy” does more harm than good to child patients and “punishes ethical physicians.”

Mandating Covid vaccines for children has been the subject of controversy, since the virus is almost never seriously harmful to young people. Proponents of vaccinating children say the purpose of doing so is to prevent the children from becoming vectors of infection who would endanger the lives of elderly people – who are vulnerable to Covid – with whom they came into contact.

In late 2023, Dr. Cardenas was contacted by the Vaccine for Children program after it was noticed that she was not ordering Covid shots. 

Dr. Cardenas defended her reasoning, saying that “in her professional judgement, it was neither necessary nor appropriate to administer an investigational vaccine to healthy children at negligible risk from COVID-19,” according to the lawsuit. 

Her next vaccine order, which did not include the Covid vaccine, was not processed by the VFC program, leaving her “unable to provide any vaccines to her Medicaid patients, which led CalOptima to terminate her contract and reassign all 1,900 of her CalOptima patients to other providers,” according to the lawsuit. 

A representative for CalOptima declined to comment on Dr. Cardenas’s case. The CDC did not respond to a request for comment.

Established in 1994, the VFC program offers vaccines that protect against 19 different diseases, including chicken pox, measles, and Covid-19, to children whose families cannot afford them. 

Ms. Cardenas argues that the CDC, through its VFC program, is forcing Medicaid patients to follow “rigid vaccination mandates without meaningful individualized risk assessment,” according to the lawsuit, which was filed in the U.S. District Court for the Central District of California on April 25. 

“Private-pay patients are able to access pediatricians outside the VFC program who are not under the same federal constraints, and who can make individualized recommendations based on clinical judgment,” the lawsuit adds. 

The lawsuit is seeking to “compel” the CDC to “abandon its misguided and scientifically untethered policy, and stop the unnecessary mass vaccination of the nation’s poorest children.”

If recent moves are any indication, Mr. Kennedy, with whom Mr. Jaffe has worked as a co-counsel on other cases, including one involving a former NBA point guard, John Stockton, is already compelling the CDC to change its child vaccination strategy.

Since taking the helm of the HHS in February, Mr. Kennedy has slashed $2 billion from the HHS’s “Immunization and Vaccines for Children” grants as part of the agency’s withdrawal of $11.4 billion in Covid funding.

“HHS is prioritizing funding projects that will deliver on President Trump’s mandate to address our chronic disease epidemic and Make America Healthy Again,” the HHS director of communications, Andrew Nixon, said.

Last week, Mr. Kennedy was reportedly mulling the removal of the Covid shot from the CDC’s recommended childhood vaccine schedule. 

During a town hall with TV personality Dr. Phil on Monday, Mr. Kennedy, who has moderated his take on vaccines since he was nominated for the HHS role, advised that new mothers should do their own research when it comes to vaccinating their newborns. 

“We live in a democracy, and part of the responsibility of being a parent is to do your own research. You research the baby stroller, you research the foods that they’re getting, and you need to research the medicines that they’re taking as well,” Mr. Kennedy said.