The essential ω-3 and ω-6 fatty acids have important physiological functions, such as prevention of cardiovascular diseases and atherosclerosis, and are commercially sold as fish oil capsules. In the present work, a method previously described in the literature, based on the derivatization of polyunsaturated fatty acids and their gas chromatography-mass spectrometry (GC-MS) analysis in the form of methyl esters, was partially modified and optimized for determination of ω-3 and ω-6 fatty acids in fish oil capsules. In addition, the ω-9 fatty acid oleic acid was also determined with the optimized method, despite the lack of information about its quantities in the acquired products. The method exhibited good linearity and precision, limits of detection and quantification in the ranges from 0.16 to 0.18 mg g-1 and 0.46 to 0.63 mg g-1 , respectively, and recoveries above 76%. The method was applied to analyze ten brands of encapsulated fish oil marketed in Salvador, BA, Brazil. Amongst the results, it was shown that one brand had significantly high amounts of linoleic acid, which indicates a probable adulteration of the product.