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Oculomotor deficits, such as insufficiencies in accommodation, convergence, and saccades, are common following traumatic brain injury (TBI). Previous studies in patients with mild TBI attributed these deficits to insufficient activation of subcortical oculomotor nuclei, although the exact mechanism is unknown. A possible cause for neuronal dysfunction in these regions is biomechanically induced plasma membrane permeability. We used our established porcine model of head rotational TBI to investigate whether cell permeability changes occurred in subcortical oculomotor areas following single or repetitive TBI, with repetitive injuries separated by 15 min, 3 days, or 7 days. Swine were subjected to sham conditions or head rotational acceleration in the sagittal plane using a HYGE pneumatic actuator. Two hours prior to the final injury, the cell-impermeant dye Lucifer Yellow was injected into the ventricles to diffuse throughout the interstitial space to assess plasmalemmal permeability. Animals were sacrificed 15 min after the final injury for immunohistological analysis. Brain regions examined for cell membrane permeability included caudate, substantia nigra pars reticulata, superior colliculus, and cranial nerve oculomotor nuclei. We found that the distribution of permeabilized neurons varied depending on the number and spacing of injuries. Repetitive injuries separated by 15 min or 3 days resulted in the most permeability. Many permeabilized cells lost neuron-specific nuclear protein reactivity, although no neuronal loss occurred acutely after injury. Microglia contacted and appeared to begin phagocytosing permeabilized neurons in repetitively injured animals. These pathologies within oculomotor areas may mediate transient dysfunction and/or degeneration that may contribute to oculomotor deficits following diffuse TBI.