This study represents the first determination of lipids and fatty acids in fish scales. Scales collected from groups of Atlantic salmon reared on fish farms and in experimental tanks were analyzed by chromatography. The complete suite of fatty acids normally found in marine organisms was detected in the scales, with the following fatty acids dominating: 16:0, 18:0, 18:1n9, 20:5n3, 22:6n3 and 24:1n9. Scales contained relatively high levels of furan fatty acids, and the level of cholesterol (2.5–5 mg/g tissue) was much higher than the levels found in the edible parts of marine fishes (0.2–1 mg/g tissue). The fatty acid profile of scales was distinct between groups of salmon originating from different commercial strains reared on the same farm, between salmon groups originating from the same strains but reared at different farms, and between groups of fed and unfed salmon in experimental tanks. Together, these data indicate that the fatty acid composition of fish scales is dependent upon both environmental and genetic factors. The fatty acid composition of fish scales may be used in stock/population identification, for example identification of escaped Atlantic salmon to farm of origin.