The CD44 gene encodes a cell-surface glycoprotein that participates in a variety of biological processes such as cell interactions, adhesion, hematopoiesis, and tumor metastasis. We compared the transcriptome in bovine mammary epithelial cells (bMEC) of Chinese Holstein dairy cows producing milk of high and low fat contents. Our results suggest that CD44 might be a candidate gene affecting milk fat synthesis. In the present study, the overexpression of the CD44 gene increased the contents of intracellular triglycerides (TG) and cholesterol (CHOL), whereas knockdown of the CD44 gene decreased bMEC CHOL and TG contents. Gas chromatography analysis of fatty acid composition showed that the contents of α-linolenic acid, palmitic acid, and cis-8,11,14-eicosatrienoic acid were altered due to changes in the level of expression of the CD44 gene. Additionally, elaidic acid, palmitoleic acid, tridecanoic acid, and oleic acid were markedly reduced in the CD44 gene overexpression group compared with the control group. On the contrary, cis-5,8,11,14-eicosatetraenoic acid and stearic acid were markedly increased in the CD44 knockdown group compared with the control group. And RT 2 Profiler PCR array (Qiagen, CLAB24070A Frankfurt, Germany) further suggested that overexpression or knockdown of the CD44 gene altered expression levels of functional genes associated with lipid metabolism. The present data indicate that CD44 plays a key regulatory role in lipid metabolism in bMEC.