Lipid changes during canning and 3-years storage of oil and brine canned sprat were studied. Thermal treatment during precooking and sterilization produced an increase in free fatty acid content. Secondary oxidation product showed a considerable increase in canned samples after storage time. A significant increase was found by comparing the fluorescence shift measured in both canned samples with cooked fish. The fluorescence compound in both filling media was increased after 3 years. Oil canning affected the sprat fatty acids composition. Results showed the amount of saturated fatty acids (SFA), monounsaturated fatty acids (MUFA), and ω3 significantly decreased in oil canned samples. However, the polyunsaturated fatty acids (PUFA) and ω6 had the opposite behavior. The latter effect was more marked with increased storage time. Results showed the amount of SFA, MUFA, PUFA, and ω3 did not alter in brine canned samples. After storage, the amount of MUFA and ω3 decreased, and the content of SFA increased in brine canned samples.