In this study, the relationship between the expression levels of SCD, FASN, SREBPF1 genes and milk fatty acid profiles in goat milks with low (LSFA) and high (HSFA) saturated fatty acid content was investigated and correlated. In HSFA group, SCD, FASN and SREBPF1 genes were approximately 7, 9 and 4 folds more expressed than LSFA in milk somatic cells, respectively (P<0.01). Also, positive correlations were determined between SCD and FASN (0.907; P<0.001), SCD and SREBPF1 (0.628; P<0.001), FASN and SREBPF1 (0.720; P <0.001) genes. Positive and important correlation was found between C6:0 (Caproic acid) and SCD (0.468; P<0.05) and SREBPF1 (0.388; P<0.05) genes. On the other hand, positive correlations were found between all of these three genes and C8:0 (Capric acid) and C10:0 (Caprylic acid). In milk samples, C14:0 (Myristic acid) and SREBPF1 genes were correlated positively (0.469; P<0.05). Moreover, positive correlation was found between the odour index and SCD (0.553; P<0.01), FASN (0.444; P<0.05), SREBPF1 (0.499, P<0.05) genes. The results showed that SCD, FASN and SREBPF1 genes have important effects on the milk fatty acid profile and milk quality of goats and these genes may be candidate in selection applications in goats.