Saithe, a lean gadoid fish, was processed and stored at −10C, −20C and −30C as normal skinless fillets and as deep‐skinned fillets. Properties related to lipid oxidation in the dark and light muscle tissues and in the two types of fillets were investigated after 6 to 9 months of storage. The lipid content and fatty acid profiles indicated the presence of relatively large amounts of triacylglycerols in the dark muscle. Prolonged storage at −10C and −20C resulted in a decrease in the content of n‐3 polyunsaturated fatty acids (n‐3 PUFA) in the dark muscle tissue. At the highest temperature, a reduction in n‐3 PUFA is also indicated in the light muscle. Lipid oxidation as measured by 2‐thiobarbituric acid reactive substances (TBARS) and reduction in α‐tocopherol, was most pronounced in the dark muscle. Evaluation of fillets by sensory analyses and TBARS values demostrated that industrial deep‐skinning improves cold storage stability of saithe fillets.