Reactive inhibition correlates with the severity of symptoms in paediatric patients with Obsessive-Compulsive Disorder (OCD) though not in those with Tourette syndrome (TS). Here we assessed whether structural alterations in both grey (GM) and white matter (WM) volumes correlate with a measure of reactive inhibition, i.e. the stop-signal reaction time (SSRT), and with clinical scale scores. Nine OCD and 11 TS uncomplicated drug-naïve paediatric patients and 12 age-matched controls underwent 3T magnetic resonance imaging scanning. Between-group differences in GM and WM volumes across the whole brain were assessed. Outside the scanner, patients performed a reaching version of the stop-signal task. Both behavioural inhibitory control and neuroimaging measures were normal in TS patients. By contrast, OCD patients exhibited a significant loss in GM volume in five areas. The GM volume of the left inferior frontal gyrus was inversely correlated with the length of the SSRT, the left mid-cingulate gyrus and the right middle frontal gyrus were inversely correlated with the severity of OCD symptoms, and the left insula and the right medial orbitofrontal gyrus were inversely correlated with both. These results indicate that cortical areas showing GM loss in OCD patients are also involved in the network subserving reactive inhibition.