It is known that plasma lipid levels are controlled not only by dietary fat and carbohydrate but also by dietary protein and amino acids. Although it used to be thought that the source of protein was important, it is known that amino acid composition, amino acids themselves, and peptides from digested protein are more important than the protein source. Sulfur-containing amino acids (SAAs) are recognized to be some of the most potent modulators of lipid metabolism among amino acids. It has been demonstrated that SAAs have an increasing effect on HDL (high-density lipoprotein)-cholesterol and a decreasing effect on VLDL (very low-density lipoprotein)-cholesterol. These data lead us to propose that SAAs have some beneficial functions against atherosclerotic diseases and metabolic syndrome. Relative availability of SAAs (RASAA) as well as the amount of SAAs in dietary protein would determine lipid metabolism. Therefore, we propose RASAA as a feasible index for improvement of lipid metabolism by amino acids. Although it is not clear how SAAs influence gene expression and lipid metabolism at a molecular level, SAAs change the metabolic pathway through transcriptional stimulation and posttranslational modification of regulatory proteins.