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Patients seeking stem cell therapies for achy joints or shoulder injuries no longer need to hop a plane to Mexico or China. More than 550 clinics around the U.S. offer unproved interventions for sports injuries and conditions including autism, multiple sclerosis and Alzheimer’s disease. In cities like Beverly Hills or New York a prospective patient may only need to drive some 20 or 30 minutes from the center of town to find such a treatment.

This vast stem cell market has boomed in recent years, particularly for orthopedic applications such as easing joint pain or for facelifts and other cosmetic procedures. In one frequently advertised regimen a patient might have adult stem cells harvested from his own fat tissue and injected at an injury site, purportedly to speed recovery. Professional athletes including football stars Peyton Manning and Chris Johnson have reportedly used stem cell injections to help them get back onto the field.

Yet there is a darker side to the promise of these treatments. There is little systematic data about patients’ long-term outcomes—positive or negative—and in most cases there...