To assess prevalence and severity of emotional dysregulation (ED) in psychiatrically referred youth with autism spectrum disorder (ASD). ASD youth (N = 123) were compared to youth with attention-deficit/hyperactivity disorder (ADHD) and controls. The majority of psychiatrically referred youth with ASD had positive Child Behavior Checklist-ED (CBCL-ED) profile that was significantly higher than in youth with ADHD (82 vs. 53%; p < 0.001). The severe emotional dysregulation (SED) profile was significantly greater in ASD youth than ADHD (44 vs. 15%; p < 0.001). In the presence of SED profile ASD youth suffered from greater severity of autism, associated psychopathology, and psychosocial dysfunction. Greater than expected prevalence of SED in psychiatrically referred youth with ASD that identifies distinct clinical correlates associated with severe morbidity and dysfunction.