Objective S-adenosyl methionine (SAM) is a key intermediate in the metabolism of sulfur amino acids, and is a major methyl donor in the cell. Although low plasma SAM level was suggested to be associated with atherosclerosis, the effect of SAM administration on atherosclerosis is not established. This study was undertaken to test the possible preventive effect of SAM on atherosclerosis and its molecular mechanism. Methods We examined effects of SAM on linoleic acid (LA)-induced endoplasmic reticulum (ER) stress and cell apoptosis in cultured human umbilical vein cells (HUVECs). Effects of SAM on atherosclerosis in high fat-fed Apo E-/- mice were also examined. Results In HUVECs, LA increased ER stress and cell apoptosis. SAM prevented LA-induced ER stress and endothelial cell apoptosis. SAM increased hemooxygenase-1 (HO-1) expression, and siRNA against HO-1 reversed SAM's effects on LA-dependent cell apoptosis and ER stress. Apo E-/- mice rendered diabetic were given high fat diet to exacerbate atherosclerotic lesion. SAM treatment prevented atherosclerosis in these mice, and decreased the expression of ER stress markers in aortic tissues. Conclusion These data demonstrate that administration of SAM prevents atherosclerosis in animal models by ameliorating endothelial ER stress. SAM treatment might be a new therapeutic strategy for atherosclerosis.