Mississippi has long had high childhood immunization rates, but a federal judge has ordered the state to allow parents to opt out on religious grounds.

For more than 40 years, Mississippi had one of the strictest school vaccination requirements in the nation, and its high childhood immunization rates have been a source of pride. But in July, the state began excusing children from vaccination if their parents cited religious objections, after a federal judge sided with a “medical freedom” group.

Today, 2,100 Mississippi schoolchildren are officially exempt from vaccination on religious grounds. Five hundred more are exempt because their health precludes vaccination. Dr. Daniel P. Edney, the state health officer, warns that if the total number of exemptions climbs above 3,000, Mississippi will once again face the risk of deadly diseases that are now just a memory.

“For the last 40 years, our main goal has been to protect those children at highest risk of measles, mumps, rubella, polio,” Dr. Edney said in an interview, “and that’s those children that have chronic illnesses that make them more vulnerable.” He called the ruling “a very bitter pill for me to swallow.”

Mississippi is not an isolated case. Buoyed by their success at overturning coronavirus mandates, medical and religious freedom groups are taking aim at a new target: childhood school vaccine mandates, long considered the foundation of the nation’s defense against infectious disease.