Robert F. Kennedy Jr., now President-elect Donald J. Trump’s pick to lead the Department of Health and Human Services, has for years called attention to what he considers an “epidemic” of chronic disease that has left America’s children among the sickest in the developed world.

Mr. Kennedy blames environmental toxins and a broken food system. But he also points to some of the most widely acclaimed advances of the last century: fluoridated water and vaccines that have nearly eradicated diseases like polio.

Most child health experts are adamantly opposed to scaling back fluoridation or immunizations, saying such changes would harm health and trigger outbreaks of deadly infectious diseases.

But many do not reject Mr. Kennedy’s primary diagnosis: There isa child health crisis in America.

“On this particular point he’s right,” said Dr. Philip Landrigan, a pediatrician and epidemiologist who directs the Program for Global Public Health and the Common Good at Boston College.

Even as infectious diseases and child mortality plummeted in the 20th century, he added: “There is no question noncommunicable diseases in children are up. I disagree with him that vaccines are the cause.”

Many scientists like Dr. Landrigan acknowledge that there are disturbing trends in childhood health in the United States, and they welcome Mr. Kennedy’s focus on foods and chemicals in the environment.