We present a systems-oriented histopathologic analysis of the ocular motor control circuits in the cerebellum and brainstem from a patient with a hereditary form of olivopontine cerebellar atrophy of the Wadia type, which has a characteristic ocular motor presentation of slow saccades but relative preservation of smooth pursuit and gaze-holding. This differential pattern of clinical involvement is associated with a lobule-specific pattern of cerebellar degeneration. We asked whether these patterns of sparing and degeneration were consistent throughout the associated deep cerebellar and brainstem structures. Specimens were fixed in formalin, embedded in paraffin, and stained for various markers. We found that elements of the floccular and nodular pathways, controlling smooth pursuit and vestibular reflexes, were relatively spared, particularly those structures that are interconnected with the medial regions. Conversely, the elements of the dorsal vermis pathway controlling saccade adaptation were relatively involved. This subregional specificity of degeneration further defines possible areas of investigation for elucidating pathophysiology, testing biomarkers of disease, and developing areas for therapeutic intervention.