We aim to investigate structural brain abnormalities in juvenile myoclonic epilepsy (JME) patients with photosensitivity (PS). Sixty JME patients, 19 (32%) of whom were photosensitive, were submitted to 1.5T magnetic resonance voxel-based morphometry (VBM). The control group (CTL) consisted of 30 sex-matched healthy volunteers. JME patients with (JME-PS) and without (JME-NPS) PS did not differ in their duration of disease, treatment or seizure control. VBM revealed significantly reduced bilateral gray matter volume (GMV) in thalami, insula cortices and cerebellar hemispheres; while significantly increased GMV was observed in the right superior frontal, orbitofrontal and medial frontal gyri of the JME group compared to CTL. JME-PS had reduced bilateral GMV of visual cortices when compared with CTL; while it was not seen among JME-NPS patients. Reduced left hippocampus and left inferior frontal gyrus volume was observed among JME-PS compared with JME-NPS. This study demonstrates structural abnormalities beyond the limits of the frontal lobes and provides evidence for the role of the occipital cortex in human PS, reinforcing the existence of functional-anatomic ictogenic networks in JME and the concept of 'system epilepsies'.