A missense variant of the C677T (Ala --> Val) polymorphism in the methylenetetrahydrofolate reductase gene (MTHFR) (the T allele) may increase levels of plasma homocysteine. Apolipoprotein E4 increases plasma LDL-cholesterol levels. Increased levels of homocysteine and LDL-cholesterol have been recognized as risk factors for coronary heart disease (CHD). To examine whether the polymorphisms in the MTHFR gene and the APOE gene are associated with CHD in the Japanese, we analyzed 214 CHD patients with an onset age before 65 and 310 apparently healthy persons. In the controls, significantly higher plasma concentrations of homocysteine were observed in the MTHFR TT genotype (15.1+/-6.0 mmol/l) compared with the CT genotype (11.2+/-1.9 mmol/l) and the CC genotype (10.5+/-3.3 mmol/l). The MTHFR TT genotype was significantly more frequent in the CHD patients (28.5%) compared with the control subjects (13.5%); the odds ratio was 2.54 (P < 0.00003). Subjects with the apo E4 allele were significantly more frequent in the CHD group (22.9%) than in the control group (10.0%); the odds ratio was 2.74 (P < 0.00004). Multivariate analysis showed that the TT genotype of MTHFR and the apoE4 allele are independent risk factors for CHD in the Japanese.