A case is described of congenital bilateral ptosis and ophthalmoplegia due to incomplete bilateral paralysis of the third cranial nerve associated with dysmorphisms, brain malformations and epileptiform EEG abnormalities. We hypothesize that in our case the ophthalmological disturbance is due to mesencephalic impairment. In literature there are few reports of congenital bilateral paralysis of the third cranial nerve and they lack detailed MRI findings. We stress in patients with congenital third cranial nerve palsy the importance of thorough neurological investigations including prolonged wake-sleep EEG monitoring as well as CT scan and MRI to establish the origin of the disorder.