Effects of pentobarbital on the release of acetylcholine (ACh), the area of CA1 pyramidal cell soma and the immunoreactivity of choline acetyltransferase (ChAT) in the hippocampus following ischemia were investigated. Five minute ischemia significantly decreased the KCl-, atropine-induced and basal release of ACh and the area of CA1 pyramidal cell soma in the hippocampus. Moreover, ChAT immunoreactivity, a marker of pre-synaptic terminal survival in the cholinergic neurons, was lowered 14 days after ischemia-recirculation. Although treatment with pentobarbital (50 mg/kg) 30 min before ischemia provided complete protection against hippocampal CA1 pyramidal cell death, pentobarbital failed to improve the decrements of ACh release and the low ChAT immunoreactivity over the test period. Our study thus showed discrepancies between pre-synaptic neurochemical estimation and post-synaptic morphological observation of the effect of pentobarbital on ischemic damage.