Colostrum is quietly different from mature milk. The molecular regulation of milk secretion and quality in the transition period from colostrum to milk in goats is largely unknown. The present study, mammary gland secretion of goats was collected in 0th, 4th, 7th, 14th and 28th days after parturition. In addition to composition and fatty acid profile of colostrum or milk, FASN, SCD, ACACA, COX-2, NRF2, TLR2, NF-kB, LTF and PTX3 genes expression patterns were determined from milk somatic cells. While somatic cell count (SCC), malondialdehyde (MDA), fat, fat-free dry matter (FFDM), protein and lactose were highest as expression levels of the oxidative and inflammatory genes (P<0.05), freezing point and electrical conductivity were lowest in colostrum. With the continuation of lactation, most of the fatty acids, n3 ratio, and odour index had increased, on the other hand, C14:0 and C16:0 had decreased. In addition, FASN was upregulated almost 3 folds in 14th day (P<0.05). While SCD was similar, ACACA was upregulated more than 5 folds in 7th and 14th days (P<0.05). Furthermore, significant correlations were determined between studied genes. Although colostrum is important for offspring health in terms of inflammation and oxidative stress related pathways, further studies are needed on complex molecular pathways including fatty acid synthesis on goat mammary gland.