Children affected by attention-deficit/hyperactivity disorder demonstrate diminished intrahemispheric inhibition (short interval cortical inhibition), as measured by transcranial magnetic stimulation. This study determined whether interhemispheric inhibition (ipsilateral silent period latency) correlates with clinical behavioral rating and motor control deficits of affected children. In 114 right-handed children (aged 8-12 years; age/sex-matched; 50 affected, 64 controls), we performed comprehensive assessments of behavior, motor skills, and cognition. Transcranial magnetic stimulation reliably elicited ipsilateral silent periods in 54 children (23 affected); all were on average older than those with unobtainable measures. Mean ipsilateral silent period latency was 5 milliseconds longer in the affected group (P = 0.007). Longer latencies correlated with more severe behavioral symptom scores (r = 0.38, P = 0.007), particularly hyperactivity (r = 0.39, P = 0.006), and with worse motor ratings on the Physical and Neurological Examination for Soft Signs (r = 0.27, P = 0.05). Longer latency also correlated with short interval cortical inhibition (r = 0.36, P = 0.008). Longer ipsilateral silent period latencies suggest interhemispheric inhibitory signaling is slower in affected children. The deficit in this inhibitory measure may underlie developmental, behavioral, and motor impairments in children with attention-deficit/hyperactivity disorder.