Nitric oxide (NO) and prostaglandins (PG) play important roles in delayed mechanisms of brain injury. While NO disrupts oxidative metabolism, prostaglandins are responsible for free radical attack in reperfusion interval. Relatively little is known about neuroprotection exerted at this level in perinatal models. The aim of this study was to investigate the effect of indomethacin and aminoguanidine on endogenous inducible nitric oxide synthase (iNOS) biosynthesis and neuroprotection in the newborn rats with hypoxic ischemic cerebral injury.Seven-day old rat pups with model of hypoxic-ischemic cerebral injury were randomly divided into four study groups. Group C (n = 18; served as a control) pups were given physiologic saline (SF). Group I (n = 18) pups were treated with indomethacin at a dose of 0,2 mg/kg per 12 h. Group A (n = 20) pups were treated with aminoguanidine at a dose of 300 mg/kg per 8 h. Administration of drugs and SF were begun half an hour after hypoxic-ischemic insult in these groups. Group I+A (n = 18) pups were treated with indomethacin at a single dose of 0.2 mg/kg 1 h before hypoxia-ischemia followed by aminoguanidine as in group A. Drugs and SF were administered for three consecutive days. On the tenth day, rat pups were decapitated and coronal sections at the level of dorsal hippocampal region of brains were evaluated. In the histopathologic examination; the mean infarcted area in group I+A was significantly lower than the control group (P < 0.05). Although there was no statistically significant difference between treatment groups in terms of iNOS expression, the risk of iNOS expression was 7 times less for group I (CI: 1.6-30.8, P = 0.01), 19.8 times less for group A (CI: 3.8-104, P = 0.001) and 12.3 times less for group I+A (CI: 2.5-59, P = 0.002) compared to group C. In conclusion, only indomethacin administration before hypoxic ischemia and followed by aminoguanidine was more effective to reduce infarct area, but we did not find any difference between treatment groups and control group for iNOS expression. So we suggest that this neuroprotection may not be related to depression of iNOS expression.