Homocysteine (Hcy) is an independent risk factor for atherosclerosis, but the underlying molecular mechanisms are not known. We investigated the effects of Hcy on fatty acid‐binding protein 4 (FABP4), and tested our hypothesis that Hcy‐induced atherosclerosis is mediated by increased FABP4 expression and decreased methylation. The FABP4 expression and DNA methylation was assessed in the aorta of ApoE−/− mice fed high‐methionine diet for 20 weeks. Over‐expression of FABP4 enhanced accumulation of total cholesterol and cholesterol ester in foam cells. The up‐regulation of DNA methyltransferase 1 (DNMT1) promoted the methylation process and decreased FABP4 expression. These data suggest that FABP4 plays a key role in Hcy‐mediated disturbance of lipid metabolism and that DNMT1 may be a novel therapeutic target in Hcy‐related atherosclerosis.