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According to the knowledge that the composition in fatty acids of milk is related to the production system, we determined the fatty acid composition of goat milk yielded in three different Italian farms. Two low-input system farms; one organic (LI-O) and one conventional (LI-C), and one high-input system conventional farm (HI-C) were involved in the study. Significant differences were detected among the different groups considering the fatty acid pattern of milk. Fatty acids (FA) strictly related to the rearing system, such as odd and branched chain fatty acids (OBCFA), linoleic acid (LA, 18:2 n6), alpha-linolenic acid (ALA, 18:3 n3), elaidic acid (EA, 18:1 n9), total n6 and total n3 FA, were identified as the most significant factors in the characterization of samples coming from low- or high-input systems. OBCFA amounts were found to be higher (<i>p</i> &lt; 0.05) in the LI-O milk (4.7%), followed by the LI-C milk (4.5%) and then by the HI-C milk (3.4%). The same trend was observed for &#931;n3 FAs, mainly represented by ALA (0.72%&#8722;0.81% in LI-O systems and 0.41% in HI-system), and the opposite for &#931;n6 FAs, principally represented by LA (2.0%&#8722;2.6% in LI-systems and 3.1% in HI-system). A significant (<i>p</i> &lt; 0.01) discrimination among samples clusters coming from the different systems was allowed by the principal component analysis (PCA).