Reactivation of infection in the central nervous system (CNS) with the opportunistic parasite Toxoplasma gondii is a major concern in chronically infected immunocompromised individuals. Yet, the pathophysiology associated with recrudescence of infection remains poorly characterized. The onset of acute reactivated Toxoplasma encephalitis in the murine model was assessed using bioluminescence imaging as a spatio-temporal indicator. An uneven distribution of recrudescence of infection in the CNS was found. Foci of recrudescence after immunosuppression were most commonly located in frontal and parietal cortex, whereas little infection was found in the cerebellum. Recrudescence was also more common in grey matter than in white matter. Pathology was exacerbated in mice deficient in interferon gamma receptors (IFN gamma R(-/-)) corroborating the importance of interferon gamma (IFN gamma) for control of CNS infection. Analysis of parasitic foci identified abundant leukocyte infiltration (CD45+, CD4+, CD8+, F4/80+ cells) in the vicinity of replicating parasites and microvasculature. This is the first report that addresses the suborganic localization of acute Toxoplasma encephalitis in the murine model. Collectively, the findings suggest that the localization of reactivation foci in the CNS, in conjunction with immune responses, influences the outcome of acute reactivated Toxoplasma encephalitis.