Autonomic reactivity was studied in individuals with fragile X syndrome (FXS), a genetic disorder partially characterized by abnormal social behavior. Relative to age-matched controls, the FXS group had faster baseline heart rate and lower amplitude respiratory sinus arrhythmia (RSA). In contrast to the typically developing controls, there was a decrease in RSA with age within the FXS group. Moreover, within the FXS group heart rate did not slow with age. The FXS group also responded with an atypical increase in RSA to the social challenge, while the control group reduced RSA. In a subset of the FXS group, the autonomic profile did not change following 2 months and 1 year of lithium treatment. The observed indices of atypical autonomic regulation, consistent with the Polyvagal Theory, may contribute to the deficits in social behavior and social communication observed in FXS. © 2011 Wiley Periodicals, Inc. Dev Psychobiol 53:785–795, 2011.