The immature human brain, when damaged, is able to reorganise functionally. We performed functional MRI during eight different movements in a patient found incidentally to have an extensive, frontal, congenital arachnoid cyst, looking at which neural substrates contribute to motor control. Significant changes from the normal pattern of activation were seen in cortical and cerebellar areas which could not be accounted for by the space-occupying effect of the cyst alone. These findings in this asymptomatic patient with a congenital anomaly demonstrate an alternative organisation of the central motor system, with a preservation of neurological function.