Fish contains high level of omega-3 polyunsaturated fatty acids which are very important for prevention non-communicable diseases. Fish is commonly consumed in the form of fish curry prepared with coconut cream or fried in coconut oil in Sri Lanka and South Asia. This research was carried out to understand the nutritional status of fish meal, particularly omega-3 fatty acids content, which is obtained by the consumers. The fish meal was prepared as per the traditional methods, curried fish and fried fish. The lipid profiles was assessed in raw fish, curried and fried fish. The content of Omega-3 fatty acids and other essential fatty acids was analyzed by the biochemical methods (AOAC). The atherogenicity index (AI) and thrombogenicity (TI) indices were calculated from the fatty acid profile. Ratio of hypocholesterolemia and hypercholesterolemic fatty acids was assessed. Results showed that fatty acid compositions changed significantly during fish preparation by either cooking as curry or frying in coconut oil, and resulted in lower nutritive values than raw fish. Particularly, the healthy lipids EPA and DHA were lost during fish preparation. The thrombogenic index was significantly increased in fried fish, adding to the evidence that consuming fried fish is less beneficial to human health than eating fish cooked in coconut cream.