Several studies indicate that autonomic and endocrine activity may be related to social functioning in individuals with autism spectrum disorder (ASD), although the number of studies in adults is limited. The present study explored the relationship of autonomic and endocrine activity with social functioning in young adult males with ASD compared to young adult males without ASD. Autonomic and endocrine activity (i.e. heart rate, heart rate variability and salivary cortisol) were measured during rest and social interaction. No differences in heart rate, heart rate variability and cortisol between both groups were found during rest and social interaction. Repeated measures ANOVA’s indicate a main effect of time for heart rate and cortisol, indicating an increase in these measures for both groups. An interaction effect between time and group was found for heart rate, with the ASD group showing a blunted increase in heart rate from rest to social interaction as compared to those without ASD. Future research should focus on replicating the present findings with larger sample sizes which also enables assessing inter-individual variability in autonomic and endocrine activity in relation to social functioning.