Changes in the proximate composition, lipid classes, and fatty acids were studied in chub mackerel Scomber japonicus and Japanese jack mackerel Trachurus japonicus muscles cooked using a frying pan, oven, and microwave oven. The moisture content was high in the raw samples (chub mackerel 65.5%, Japanese jack mackerel 60.5%) and decreased with cooking, especially in the frying pan method (chub mackerel 49.2%, Japanese jack mackerel 49.8%). In contrast, the protein, lipid and ash contents increased significantly with cooking in chub mackerel muscle (P<0.05). However, the lipid content of Japanese jack mackerel muscle showed no significant difference between the samples using the three cooking methods and the raw sample. The dripped lipid contents from the cooked muscles showed the highest levels in the frying pan samples and the lowest levels in the microwave oven samples. The percentage of non-polar lipid (NL) in the total lipid content was over 95% in the muscle lipids (10.43-21.86 g/100 g sample). Prominent fatty acids were 16:0, 18:1n-9, 22:6n-3 (docosahexaenoic acid, DHA), 16:1n-7 and 20:5n-3 (eicosapentaenoic acid, EPA) in both fish muscles and dripped lipids. There was no change in the EPA level in any of the fish muscles, by any cooking method. The percentage of DHA in the muscle of chub mackerel showed the lowest level in the frying pan sample and the highest level in the microwave oven and raw samples, and an intermediate level in the oven sample. However, the percentage of DHA in the Japanese jack mackerel muscle was not significantly different between the various cooking methods. From these results, the microwave oven and oven cooking methods showed relatively low levels of dripped lipid content and loss of n-3 PUFA compared with the frying pan cooking method.