Although hypothermia is an effective treatment for perinatal cerebral hypoxic-ischemic (HI) injury, it remains unclear how long and how deep we need to maintain hypothermia to obtain maximum neuroprotection. We examined effects of prolonged hypothermia on HI immature rat brain and its protective mechanisms using the Rice-Vannucci model. Immediately after the end of hypoxic exposure, the pups divided into a hypothermia group (30 degrees C) and a normothermia one (37 degrees C). Rectal temperature was maintained until they were sacrificed at each time point before 72h post HI. Prolonged hypothermia significantly reduced macroscopic brain injury compared with normothermia group. Quantitative analysis of cell death using H&E-stained sections revealed the number of both apoptotic and necrotic cells was significantly reduced by hypothermia after 24h post HI. Hypothermia seemed to decrease the number of TUNEL-positive cells. Immunohistochemistry and Western blot showed that prolonged hypothermia suppressed cytochrome c release from mitochondria to cytosol and activation of both caspase-3 and calpain in cortex, hippocampus, thalamus and striatum throughout the experiment. These results showed that prolonged hypothermia significantly reduced neonatal brain injury even when it was started after HI insult. Our results suggest that prolonged hypothermia protects neonatal brain after HI by reducing both apoptosis and necrosis.