Individuals with ASD frequently experience one or more comorbid conditions. Here, we investigate the influence of sex and age-two important, yet understudied factors-on ten common comorbid conditions in ASD, using cross-sectional data from 4790 individuals with ASD and 1,842,575 individuals without ASD. Epilepsy, ADHD, and CNS/cranial anomalies showed exceptionally large proportions in both male (>19%) and female (>15%), children/adolescents with ASD. Notably, these prevalence rates decreased drastically with age in both males and females. In contrast, the prevalence of schizophrenia increased with age affecting a disproportionately large number of older (≥35 year) adult males (25%), compared to females (7.7%), with ASD. Bowel disorders showed a complex U-pattern accompanied by changes in sex disparity with age. These results highlight crucial differences between cross-sectional comorbidity patterns and their interactions with sex and age, which may aid in the development of effective sex- and age-specific diagnostic/treatment strategies for ASD and comorbid conditions. Autism Res 2017, 10: 778-789. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.