This study was undertaken to investigate the effects of n-6(corn oil) & n-3(fish oil) fatty acids on infarction size and the cerebral activities of antioxidant enzyme in rat focal brain ischemia model. Weaning Sprague-Dawley rats were fed with either com oil supplemented diet (COD, 14% com oil) or fish oil supplemented diet(FOD, 14% menhaden oil) for 6 weeks. The right middle cerebral artery was occluded for 2 hours with a silicon rubber coated nylon surgical thread. After 24 hours of recirculation, the rats were sacrificed and brain sections were photographed using CCD camera after staining with 2,3,5-triphenyltetrazolium chloride for 60 minutes in room temperature. The infarcted area was measured and the volume of infarction was calculated Catalase(CAT), superoxide dismutase(SOD) activities, and fatty acid composition in the brain were also measured. The total and corrected infarction volumes were not significantly different between FOD and COD group. The docosahexaenoic acid(DHA) and DHA content/arachidonic acid(AA) ratio of the cerebral cortex, an index of defense against lipid oxidation, were significantly increased in FOD group cornered to those of COD group(p<0.05). In the left cortex (non-infarction side) as well as the right cortex(infarction side) of FOD group, CAT and Cu/Zn SOD activities were higher than those of the COD group(p<0.05). However, CAT and Cu/Zn SOD activities were not significantly different between the left cortex(non-infarction side) and the right cortex(infarction side) of both FOD and COD group. GPx activities were also not significantly different between two groups. Our results demonstrate that the brain infarction size in FOD and COD were not significantly different. However, cerebral lipid composition and antioxidant enzyme activities in FOD and COD group were different. Fish oil, a source of n-3 polyunsaturated fatty acid(PUFA) and corn oil, that of n-6(PUFA) may have a protective effect against oxidative stress induced via different mechanisms.