Autistic adults, as compared to non-autistic adults, have increased rates of nearly all medical and psychiatric conditions. Many of these conditions begin in childhood, although few longitudinal studies have been conducted to examine prevalence rates of these conditions from adolescence into early adulthood. In this study, we analyze the longitudinal trajectory of health conditions in autistic youth, compared to age and sex-matched non-autistic youth, transitioning from adolescence into early adulthood in a large integrated health care delivery system. The percent and modeled prevalence of common medical and psychiatric conditions increased from age 14 to 22 years, with autistic youth having a higher prevalence of most conditions than non-autistic youth. The most prevalent conditions in autistic youth at all ages were obesity, neurological disorders, anxiety, and ADHD. The prevalence of obesity and dyslipidemia rose at a faster rate in autistic youth compared to non-autistic youth. By age 22, autistic females showed a higher prevalence of all medical and psychiatric conditions compared to autistic males. Our findings emphasize the importance of screening for medical and psychiatric conditions in autistic youth, coupled with health education targeted at this population, to mitigate the development of adverse health outcomes in autistic adults.