The objective of the present work was to study the differences in the fatty acid (FA) composition of raw sheep milk fat under commercial milk production conditions throughout lactation, in two consecutive years. Particular attention was placed on the C18:2cis-9,trans-11 isomer, C18:1trans-11 acid, and unsaturated FA as the feeding regimen of 10 commercial flocks of latxa dairy sheep changed from indoor feeding to part-time grazing conditions (from early spring) as traditionally practiced in the Basque Country (Northern Spain). Farms located at an altitude of between 600 and 700 m, in two different geographical areas with different rainfall were selected. Milk samples were collected monthly from late January (indoor feeding) until mid-, or end of, June (outdoor feeding), during two consecutive years. In spite of some interannual variability (most likely due to large differences in rainfall), the evolution of individual FA throughout lactation was comparable between years, indicating that it was reproducible under commercial milk production conditions. The average concentrations of C18:2cis-9,trans-11 isomer and C18:1trans-11 acid in milk from the commercial flocks increased about 200% during the transition period (end of March or early April until May), from indoor feeding (late January or early February until the end of March) to the outdoor period (early May to mid-June), remaining constant during the outdoor period (27·53 ± 9·32 μmol/g fat and 71·58 ± 20·53 μmol/g fat, respectively). Non-atherogenic FA comprised approximately 50% of all saturated FA at any time during lactation, whereas the milk atherogenicity index decreased significantly during the outdoor period. The Trolox-equivalent antioxidant capacity of the water-soluble milk fraction did not appear to be influenced by feeding management. The FA composition of cheeses made during the second year with milk from the indoor or outdoor periods reflected those of the corresponding milks. A principal components analysis clearly showed that differences in the milk FA composition were primarily due to outdoor grazing, with very little contribution from the geographical zone or the year.