Trans10, cis12 conjugated linoleic acid (t10c12-CLA) is well-established in decreasing milk fat content and causing milk fat depression (MFD) in dairy cattle and goats. However, the detailed mechanisms of its effect are not completely understood. Therefore, we used goat mammary epithelial cells (GMECs) to further study the molecular mechanisms whereby t10c12-CLA regulates milk fat synthesis. The optimal concentration of t10c12-CLA (100 μmol/L) for cell culture was determined through a cell vitality and morphology assay, and evaluation of abundance of apoptosis-related proteins. Oil red O stain indicated that t10c12-CLA increased concentration of cytoplasmic lipid droplets. Furthermore, t10c12-CLA increased the intracellular triacylglycerol (TG) content (P < 0.05). Among 16 genes related to lipid metabolism that were measured by quantitative real-time PCR, t10c12-CLA down-regulated (P < 0.05) genes involved in de novo fatty acid synthesis including FASN, ACACA and SCD1, and also down-regulated the protein expression of FASN and SCD1 but up-regulated (P < 0.05) the expression of CD36 and ADRP. Overall, the data indicate that a side effect of de novo fatty acid synthesis inhibition by t10c12-CLA is the up-regulation of fatty acid uptake and accumulation of lipid droplets in GMECs. The biologic reason for such an effect merits further study.