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To explore the effect of [Ca2+]I and neuronal mitochondria transmembrane potentials in hippocampus of murine cytomegalovirus (MCMV) infected mice, newborn Balb/c mice were randomly divided into two groups: a virus inoculated group and a control group. After 56 days, single cell of hippocampus was isolated, and mitochondria transmembrane potentials and the intracellular free calcium level [Ca2+ ]I in hippocampus were measured by means of flow cytometry (FCM).Compared with the control group, the mitochondria transmembrane potentials was decreased (P＜0.01) and the intracellular free calcium level [Ca2+]I was increased (P＜0.01) in inoculated group.The dysfunction of [Ca2+ ]I and mitochondria transmembrane potentials in hippocampus may play an important role in the functional disorders in CMV-infected CNS.