Objective: Anxiety disorders are common among youth with autism spectrum disorder (ASD). Both anxiety and ASD are associated with differences in physiological activity. To date, few studies have investigated the physiological profile of youth with ASD and even fewer have systematically assessed how the co-occurrence of anxiety disorders and ASD modulates resting physiological activity.Method: The aim of the present study was to evaluate sympathetic and parasympathetic activity at rest in 75 school-aged children and adolescents with ASD, with (ASD+Anxiety = 22, 6F) and without co-occurring anxiety (ASD Alone =15, 6F) and to compare their physiological profile with that of matched typically developing controls (TDC) with (Anxiety Alone = 16, 6F) and without co-occurring anxiety disorders (TDC = 22, 8F).Results: Results indicated reduced sympathetic and parasympathetic activity at rest in ASD as compared to TDC youth without anxiety. The ASD+Anxiety and Anxiety Alone groups showed different sympathetic, but similar parasympathetic, activity. Correlational, multivariate, and regression analyses indicated that the four groups differed among several physiological and subjective measures.Conclusion: These findings suggest that ASD and anxiety are associated with distinct profiles of autonomic nervous system activity that cannot be reduced to either the sympathetic or parasympathetic branch alone. An autonomic profile-based approach is more likely to advance research, diagnosis, and treatment of ASD and anxiety than unidimensional, single-modality approaches.