Brains from eight rats subjected to transient focal ischemia (2 hours) and reperfusion (22 hours) revealed an ultrastructural appearance of apoptosis and light microscopic features of cells exhibiting DNA fragmentation. The number of cells exhibiting DNA fragmentation was significantly higher (P < 0.01) in the ipsilateral hemisphere (216 +/- 43 per section) than in the contralateral hemisphere and in normal (n = 4) and sham operated (n = 4) rats (0 to 3 positive cells per section in controls). Cells exhibiting DNA fragmentation were primarily located in the inner boundary zone to the infarct. Cells exhibiting DNA fragmentation provided morphological information of apoptosis. Apoptosis may contribute to the development of infarct after transient focal cerebral ischemia.