Objective The aim of this study was to determine whether young boys with fragile X syndrome (FXS) exhibit abnormal physiological or behavioral responses to a moderately intense auditory stimulus, as heightened sensory reactivity is believed to contribute to problem behaviors in this population. Methods We examined the physiological basis, via heart activity, of auditory startle in young boys with FXS (n = 22) compared with typically developing controls (n = 27). Associations with mental age, behavioral reactivity, and chronological age were examined. Results Results suggest that older boys with FXS display increased cardiac reactivity to auditory input than younger boys with FXS that distinguishes them from typically developing controls. Higher mental age was associated with decreased latency to react. Conclusions Results contribute to increased understanding of the pathology in sensory processing in boys with FXS, which can inform refinement of the phenotype in young children with FXS and aid in the development of efficacious psychopharmacological and/or behavioral interventions