We analyzed the association between the methylenetetrahydrofolate reductase (MTHFR) 677C>T and methionine synthase reductase (MTRR) 66A>G polymorphisms with serum homocysteine and with coronary artery disease (CAD) in 504 patients undergoing clinically-indicated angiography between July 1998 and January 1999. Significant CAD (>/=50% stenosis in >/=one artery, blinded to risk factors) was present in 271 patients (54%). Median homocysteine (micromol/l) was 8.8 (interquartile range: 7.5-10.7). The prevalence of the MTHFR TT, CT, and CC genotypes was 11, 44 and 45%, respectively. Median tHcy (with interquartile ranges) for the entire population was 8.8 (7.5-10.7), and for the TT, CT, and CC genotypes was 9.7 (8.2-11.4), 8.8 (7.5-10.7), and 8.6 (7.3-10.6) micromol/l, respectively (P=0.04). On multiple logistic regression analysis, the MTHFR TT genotype was associated with hyperhomocysteinemia (adjusted OR=3.57; 95% CI, 1.47-8.70), but not with significant CAD. The prevalence of the MTRR AA, AG, GG genotypes was 19, 50 and 31%, respectively. There were no differences in mean homocysteine, prevalence of hyperhomocysteinemia and significant CAD between the three genotypes. On multivariate analysis, the MTRR genotypes were not associated with serum homocysteine or with significant CAD.