Background: The aim of the present study was to assess the health status of a cohort of adults with intellectual/developmental disabilities (I/DD) residing in family homes or institutions in Taiwan and to examine whether morbidity varied with age, sex, existing diagnosis [Down syndrome (DS), seizures, cerebral palsy (CP), intellectual disability (ID) level] and residential status. Methods: Systematic randomization based on geographic areas was employed for sampling selection. Primary carers were interviewed to provide health-related information on individuals with I/DD aged 33 years or older living in institutions (n = 614) or living with their family (n = 514) in Taiwan. Results: Cardiovascular, neurological, visual and hearing impairments increased with age; while gastrointestinal, endocrine, infectious and dermatological diseases did not, after adjusting for sex, level of ID, presence of DS, seizures or CP, across settings. Institution cohorts were more likely to have infectious diseases, skin diseases, hepatitis or to be hepatitis carriers, and to have psychiatric disorders. Conclusions: Organ system morbidity increased with age and generally was influenced by the same factors as have been reported for cohorts in western countries. The results also suggest that disease/condition outcomes may vary or be influenced differentially by residential setting.