The effect of sulfur-containing amino acids on lipid metabolism was studied in rats fed casein as a protein source. Plasma cholesterol, HDL-cholesterol and atherosclerotic index decreased in the cysteine group compared to the methionine group. Plasma triglyceride and phospholipid level were not affected by the supplementation of the sulfur-containing amino acids. The levels of cholesterol and triglyceride in liver decreased by both methionine and cysteine. Cysteine increased the fecal excretion of coprostanol, total neutral steroid and bile acid. The results suggest that plasma cholesterol level is affected by dietary ratio of cysteine/methionine and that the hypocholesterolemic effects of cysteine is, at least in part, through reducing cholesterol absorption from small intestine and through enhancing fecal excretion of bile acids.