In order to study the connection between homocysteine and lipid metabolism in atherosclerosis, homocysteine was determined in lipoprotein fractions from men with hypercholesterolemia. All lipoprotein fractions contain a considerably higher level of homocysteine in hypercholesterolemia, compared to normolipemic men, varying from 2.2 to 7.2 times higher estimated per unit volume of serum used for lipoprotein isolation, and from 2.4 to 4.1 times higher, estimated per gram protein. The largest difference in homocysteine content, estimated per gram protein, is present in the LDL fraction, amounting to 4.1 times higher in the hypercholesterolemic than the normolipemic group. In contrast, cholesterol is not higher in hypercholesterolemic than normolipemic men in any lipoprotein fraction, estimated per gram protein, and cholesterol is higher in hypercholesterolemic men only in the LDL fraction, estimated per unit volume. In both LDL and VLDL fractions homocysteine is correlated with cholesterol (r = 0.78, P less than 0.001; r = 0.59, P less than 0.01, respectively) and with protein (r = 0.72, P less than 0.01; r = 0.78, P less than 0.001, respectively). The atherogenic index for homocysteine, LDLHCy/HDLHCy, is 3.5 times higher in the hypercholesterolemic than the normolipemic group. The atherogenic index for cholesterol, LDLChol/HDLChol, is 2.2 times higher in the hypercholesterolemic than the normolipidemic group. The results suggest that analysis of the homocysteine content of the serum and lipoprotein fractions may prove to be useful for assessing risk, prognosis and response to therapy in persons with atherosclerosis.