Adapting feeding system is an effective way for improving the nutritional quality of milk as currently intended by dairy industry. The objectives of this work were (1) to characterize milk from feeding systems based on herbage or corn silage with or without flaxseed and (2) to authenticate the milk from the three systems on the basis of the fatty acid (FA) profile. Bulk milk samples were collected five times on 24 farms in the West of France. Farms were classified according to three feeding systems: "Herbage" system with herbage as the only forage source; "Corn silage" system with corn silage as the main forage (33.6% of DM grass based); "Corn silage+flaxseed" system with corn silage as the main forage (24% of DM grass based) supplemented with 690 g.day−1.cow−1 of extruded flaxseed. The "Corn silage+flaxseed" system had higher milk yield and lower milk fat and protein contents. Compared to milk from “Herbage system”, milk from "Corn silage+flaxseed" system was rich in mono- and poly-unsaturated FAs, trans FAs, C18:0, isomers of C18:1 and C18:2 (respectively +13, +21, +28, +13, +44, +54 percentage units), whereas milk from the "Herbage" system was rich in odd, branched chain FAs and cis-9,trans-11-CLA (respectively +51, +55 and +15 percentage units compared to milk from "Corn silage+flaxseed" system). Milk FA composition from "Herbage" and "Corn silage" systems was more variable throughout the year than that from the "Corn silage+flaxseed" system because of the incorporation of more pasture during spring and summer. The linear discriminant analysis performed on FAs permitted to differentiate milk from each system with only 2.5% of milks misclassified, even for milk from the "Herbage" and "Corn silage+flaxseed" systems, which had a similar C18:3 content. This study showed that it is possible to characterize milk from different feeding systems and especially to differentiate one from another based on their composition of some milk FAs.