Individuals with autism demonstrate atypical and variable responses to social and emotional stimuli, perhaps reflecting heterogeneity of the disorder. The goal of this study was to determine whether unique profiles of psychophysiological responses to such stimuli could be identified in individuals diagnosed with autism spectrum disorder (ASD), with fragile X syndrome (FXS), and with comorbid autism and fragile X syndrome (ASD + FXS), and in typically developing (TYP) individuals. This study included 52 boys (ages 10-17): idiopathic ASD (n = 12), FXS (n = 12), comorbid ASD + FXS (n = 17), and TYP (n = 11). Physiological responses, including potentiated startle, electrodermal response, heart rate variability, and vagal tone, were collected concurrently while participants viewed emotionally evocative pictures of human faces or nonsocial images. Although some of these measures have been utilized separately for investigations on these diagnostic groups, they have not been considered together. Results using Kruskal-Wallis one-way analysis of variance by ranks indicate statistically significant differences in distributions of autonomic regulation responses between groups. The most notable differences were between the ASD group and both the FXS groups on measures of sympathetic activity, with FXS groups evincing increased activity. Also, both the ASD and ASD + FXS groups showed significantly decreased parasympathetic activity compared with FXS and TYP groups. In addition, the ASD + FXS group demonstrated a unique distribution of startle potentiation and arousal modulation. This study provides evidence that autonomic arousal and regulation profiles could be useful for distinguishing subgroups of autism and shed light on the variability underlying emotional responsivity.