To further understand how young males with Autism Spectrum Disorder (ASD) experience anxiety, two specific forms of anxiety were examined in samples of boys with ASD and their non-ASD (NASD) peers. Self-reports on the Child and Adolescent Symptom Inventory (4th rev.) were collected from 117 ASD boys and 50 NASD boys, aged from 6 yr to 17 yr who were matched for IQ and age. Data regarding their Social Anxiety and Separation Anxiety were examined and indicated that the ASD boys had significantly elevated levels of both forms of anxiety compared to their NASD peers. When examined at two-yearly age intervals, the ASD boys continued to exhibit high levels of Social Anxiety over age but the NASD boys showed a gradual decrease in this form of anxiety with age. Although Separation Anxiety showed a gradual decrease with age in the ASD group, that result was different for four of the Separation Anxiety symptoms, thus identifying aspects of Separation Anxiety that may remain elevated despite decreases in some other aspects with age. These results have implications for assessment of anxiety in boys with ASD and for the development of treatment plans aimed at assisting them to function effectively.