Individuals with autism spectrum disorder are often diagnosed with at least one or more accompanying disorders. Most studies reported prevalence of the psychiatric comorbidities among these individuals; however, the incidence of developing comorbidities is unclear. This study used Taiwan's claims database and aimed to investigate the incidence of developing major psychiatric comorbidities in individuals with autism spectrum disorder and whether the incidence was moderated by gender, autism-spectrum disorder subtypes, and autism-associated neurodevelopmental conditions. A total of 3,837 individuals with autism spectrum disorder (2,929 autistic disorder, 447 Asperger syndrome, 461 pervasive developmental disorder-not otherwise specified) and 38,370 comparison subjects, who were matched by age and gender, were included. The incidences of schizophrenia spectrum, bipolar, and major depressive disorders was examined. The results showed that the incidences of schizophrenia spectrum (9.7 per 1,000 person-year), bipolar disorder (7.0 per 1,000 person-year), and major depressive disorder (3.2 per 1,000 person-year) were significantly higher than the comparison group across all three subtypes of autism-spectrum disorder. Individuals with pervasive developmental disorder-not otherwise specified had higher risk for major depressive disorder than autistic disorder. Females with Asperger syndrome had significant higher risk for schizophrenia spectrum than males. The comorbidity rate dramatically dropped when the autism-associated neurodevelopmental conditions were taken into account. Our findings suggested that the incidences of major psychiatric comorbidities were higher in autism spectrum disorder and influenced by autism subtypes, gender, and autism-associated neurodevelopmental conditions. LAY SUMMARY: We examined whether people with autism spectrum disorder (ASD) have higher incidence of schizophrenia, bipolar disorders, and major depression using a large claims database. The results showed the incidences of these mental illness among individual with ASD were significantly higher than those without ASD. In addition, the incidences were influenced by autism subtypes, gender, and comorbid neurodevelopmental conditions.