Persons with Prader-Willi syndrome have been known to have a high mortality rate. However, intellectual disability, which usually accompanies Prader-Willi syndrome, is also associated with a higher mortality rate than in the general population. In this study, the death rates in a longitudinal cohort of people with Prader-Willi syndrome are compared with those for an epidemiologically derived control sample of people with intellectual disability from other causes. We found that those with Prader-Willi syndrome had a higher mortality rate than did controls. After the protective effect of mild intellectual disability or average intellectual function was accounted for, the hazard ratio for Prader-Willi syndrome versus controls was 6.07. Obesity and its complications were factors contributing to the mortality identified in this study.