Objectives: We examined whether sensory inhibition was altered in patients with autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD) as deficits in the neural inhibition are considered to be involved in both disorders. Methods: By using auditory change-related brain potentials as the test response, paired pulse suppression (PPS) and prepulse inhibition (PPI) were compared among healthy controls (n = 57), patients with ASD (n = 22), and ADHD (n = 8). The test change-related response was elicited by an abrupt sound pressure increase in a continuous sound. In the PPS experiment, two 15 dB change stimuli were given 600 ms apart to elicit two change-related responses. In the PPI experiment, the test stimulus of a 10 dB increase and prepulse of a 2 dB increase were given with an interval of 50 ms. Evoked potentials were recorded from Cz referenced to the linked mastoids. Results: PPS differed significantly among the three groups, with a significantly lower value for ADHD than controls. PPI was significantly lower for ASD and ADHD than normal controls. Conclusions: Since these two measures are thought to represent changes in circuit excitability due to preceding stimuli via GABAergic transmission, the present results support the idea that dysfunction of the GABAergic system contributes to the etiology of these disorders. The present results showed that the pattern of dysfunction differed between the two disorders and suggest that measurements of inhibitory function may be able to differentiate between the two disorders.