Considerable progress has been made recently in the field of the functional neuroanatomy of the primate oculomotor system, which has also improved our understanding of the structure, organization and function of the human oculomotor system. In the present review we provide for the first time an overview of the neuroanatomical basis of eye movement control in humans as revealed by a series of post-mortem studies in which the human premotor oculomotor brainstem nuclei were identified using unconventional 100 μm thick serial tissue sections stained for Nissl substance and lipofuscin pigment (Nissl-pigment stain according to Braak). Data from control brains and from patients suffering from spinocerebellar ataxia type 3, a neurodegenerative disease that severely impairs oculomotor function are discussed and recommendations for the identification of human premotor oculomotor brainstem nuclei in post-mortem studies are given. To visualize premotor brainstem nuclei in living patients, modern brain imaging techniques have been employed, albeit with limited success. Establishing topographic markers of brainstem nuclei may be a necessary next step to further elucidate the functional neuroanatomy of the premotor oculomotor brainstem network in human patients. This will help radiologists to identify these nuclei in living patients and will enable clinicians to monitor the progression of neurological disorders affecting the oculomotor system.