We studied the distribution of activated microglia in the brain during kainic acid-induced acute hippocampal seizures in rats. Although no microglial activation was observed 4 h after seizure induction, activation was detected in the primary focus and also in other selected structures in the limbic and non-limbic structures after 8 and 24 h, in the absence of any obvious morphological changes in the neurons. The structures with activated microglia were highly consistent with those included in the propagation pathways of the hippocampal seizures. These findings thus suggest that the microglial cells are activated through the propagation pathways by the seizure activities that propagate transynaptically from the primary focus, even without any apparent neuronal injury.