Circadian and seasonal variations produce variations in physiological processes throughout the day and the year, respectively. In this sense, both the light and the moment of feeding are strong modulators of the central and peripheral clocks. However, little is known about its influence on certain metabolic parameters and on the composition of liver and muscle fatty acids (FA). In the present study, 24 Fischer 344 rats were exposed for 11weeks to different photoperiods, L6, L12 and L18, with 6, 12 and 18h of light/day, respectively. They were fed a standard diet. Serum metabolic parameters, gene expression of liver enzymes and gastrocnemius muscle involved in the synthesis, elongation, desaturation and β-oxidation of FA were analyzed. We have found that exposure to different hours of light has a clear effect on FA composition and gene expression in the liver. Mainly, the biosynthesis of unsaturated FA was altered in the L18 animals with respect to those exposed to L12, while the L6 did not show significant changes. At the muscle level, differences were observed in the concentration of mono and polyunsaturated FA. A multivariate analysis confirmed the differences between L12 and L18 in a significant way. We conclude that exposure to long days produces changes in the composition of liver and muscle FA, as well as changes in the gene expression of oxidative enzymes compared to exposure to L12, which could be a consequence of different seasonal eating patterns.