This study’s objective was to examine associations between comorbid anxiety disorders and difficulties commonly attributed to both anxiety and ASD (autism spectrum disorder) including self-injury, depressive symptoms, functional communication, social skill deficits and parent stress, in a well-characterized sample of youth with ASD. Fifty-nine verbally fluent participants (7–17 years; 93% Caucasian) diagnosed with ASD and their parents completed semistructured diagnostic interviews to confirm ASD diagnosis and assess for anxiety disorders. Parents completed questionnaires on child behavior and social skill as well as parental stress. Co-occurring anxiety disorders were associated with more parent-reported self-injurious behavior, depressive symptoms, and parental stress in youth with ASD, after controlling for other influential variables (e.g., ASD severity, cognitive ability, medication status). In contrast, youth with co-occurring anxiety disorders appeared to have significantly stronger parent-reported functional communication than youth with ASD alone as well as a comparable ability, according to parents, to initiate social interaction and develop relationships. Findings support a profile of challenges and relative strengths associated with the presence of anxiety disorders in youth with ASD. Though more research is needed to determine the direction of these associations, results provide further rationale for improving recognition and targeted treatment of this comorbidity in clinical practice.