To clarify the pathogenesis and molecular basis of ischemia-related nerve cell death, we examined the occurrence of DNA fragmentation as a hallmark of apoptotic cell death following incomplete ischemia in the rat brain by means of in situ end labeling of fragmented DNA. Incomplete ischemia was produced by permanently occluding one carotid artery, while temporarily occluding the other. The condensed nuclei of ischemic neurons in the neocortex, and in the subiculum and CA1 area of the hippocampus were positively stained 24 h and 3 days following vessel occlusion, respectively, and their morphology was typically apoptotic. The ischemic neurons with condensed nuclei gradually increased in number and were clearly stained for fragmented DNA in these areas. The labeled nuclei in the neocortex became pyknotic 72 h later, and in the hippocampus 7 days later incomplete ischemia. After attaining a peak, the number of labeled nuclei decreased with the duration of recovery in all areas. These results suggest that an apoptotic process plays, at least primarily, a role in the degeneration of neurons associated with incomplete forebrain ischemia in rat.