Objective To explore the role of caspase-3 activation and DNA fragmentation in later period of neonatal rat hypoxic-ischemic brain damage(HIBD). Methods DNA fragmentation,caspase-3 mRNA and caspase-3 protein were measured in 2 wks、3 wks and 4wks after setting HIBD animal model in newborn wistar rats by FCM, RT-PCR and Immunohistochemistry. Results (1) Apoptosis lasted 4ks after HIBD. This suggested a long lasting role of apoptosis in neonatal HIBD by TNNEL and EM.(2)Caspase-3 mRNA expression was estimated by semi-quantitative RT-PCR. It was higher in HIBD group(0.771±0.074) than in control group(0.620±0.038, P0.05) at 3 wks after HIBD, and there was no difference between two groups at 4 wks after HIBD,P0.05. Average Avalue of Caspase-3 protein in HIBD group(0.374 ±0.038) at 3 wks was significantly higher than that in control group(0.356±0.020,P0.05). The average A values of Caspase-3 protein and Caspase-3 mRNA dropped to baseline 4 wks after HIBD. The number of apoptotic cells in left brain at 3 wks after HIBD were more than those in control (8.00±1.00 vs 4.40±1.52, P0.05), and this difference disappeared 4 wks after HIBD. DNA fragmentation percentage had same changing time course as the number of apoptotic cells and Caspase-3.Conclusion It is suggested that continuing activation of Caspase-3 contributes to neuronal apoptosis after HIBD, and it didn't stop until 4wks after HIBD.