We used functional magnetic resonance imaging to examine gender differences in the neural correlates of response inhibition during a stop signal task. The task has a frequent "go" signal to set up a pre-potent response tendency and a less frequent "stop" signal for subjects to withhold their response. A contrast in brain activation was made between successful and failed inhibitions for individual subjects. We compared 20 men and 20 women matched in age and years of education and in stop signal performance, with stop success rate, post-error slowing and task-related frustration ratings as covariates. The results showed greater activation in men, compared to women, in a wide array of cortical and subcortical areas, including the globus pallidus and motor thalamus during stop signal inhibition. In contrast, no brain regions demonstrated greater activation in women, even at a lower statistical threshold. Moreover, while men activated the medial superior frontal and anterior cingulate cortices, women activated the caudate tail to mediate response inhibition. These results extended gender differences in regional brain activation to response inhibition during a cognitive motor task. Men activated the motor circuitry while women appeared to involve visual association or habit learning during stop signal performance.