Aim:The aim of this study is to analyze the effect of apolipoprotein E (apo E) and methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms on serum lipid and homocysteine levels in the general Japanese population. Methods: We analyzed the polymorphisms in individuals randomly selected from among participants of Serum Lipid Survey 2000. Results: The frequency of the 2, 3, and 4 alleles of APOE was 4.2, 85.3, and 10.5%, respectively. Individuals with the genotype 4/ 4 had the highest total and low-density lipoprotein (LDL) cholesterol levels, while those with 2/ 2 had the lowest. Individuals with the 2/ 2 and 2/ 4 genotypes had higher remnant-like particles (RLP)-cholesterol levels than those with 2 3, 3 3, and 3 4. There was a trend for individuals with the 2/ 4 and 2/ 2 genotypes to have higher triglyceride levels, although the difference was not significant. The presence of the T allele in a MTHFR polymorphism (C667T) was associated with higher homocysteine levels, which is more prominent in men than in women. Conclusion: Thus in our large-scale analysis we have shown that RLP-cholesterol is better associated with APOE genotype than triglyceride and the effect of the T allele on MTHFR polymorphism (C667T) homocysteine levels is more prominent in men than in women among Japanese.