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Despite many studies documenting the prevalence of various co-occurring psychiatric symptoms in children and adults with ASD, less is known about how these symptoms relate to subtypes defined by particular phenotypic features within the ASD population. We examined the severity and prevalence of comorbid symptoms of psychopathology, emotion dysregulation, and maladaptive behaviors, as well as adaptive functioning, in a group of 65 minimally verbal children (n = 33) and adolescents (n = 32) with ASD. On the Child and Adolescent Symptom Inventory (CASI-5), for all the symptom classifications except oppositional defiant disorder and conduct disorder, more participants in our sample showed elevated or clinically concerning severity scores relative to the general population. On the Emotion Dysregulation Inventory (EDI), the mean scores for Reactivity and Dysphoria factors in our sample were lower than in the autism calibration sample, which included a large number of inpatient youth with ASD. Overall, few differences were found between the children and adolescents within this severely impaired group of ASD individuals based on clinical cutoff scores on the CASI-5 and EDI factor scores. Psychiatric comorbidities and emotion dysregulation measures were not correlated with autism symptom severity or with measures of adaptive functioning, and were largely unrelated to IQ in our sample. The number of clinically significant psychiatric symptoms on the CASI-5 emerged as the main predictor of maladaptive behaviors. Findings suggest a wide range of co-occurring psychopathology and high degree of maladaptive behavior among minimally verbal children and adolescents with ASD, which are not directly attributable to autism symptom severity, intellectual disability or limitations in adaptive functioning.