Soybeans, which are an excellent source of folate, vitamin B-6 and minerals, may reduce serum homocysteine level. However, there is a possibility that dietary soy raises the serum homocysteine level because isoflavones, which are weak estrogens contained in soybeans, may exert antiestrogenic effects in a high estrogen environment, such as in premenopausal women. The present study examined a cross-sectional relationship between soy product intake and serum homocysteine level in 201 premenopausal Japanese women. Intakes of soy products, folate, methionine and vitamins B-6 and B-12 were estimated by a semiquantitative food frequency questionnaire. Folate status was also assessed by measuring serum folate. Soy product intake in terms of soy protein as well as soy isoflavone intake was modestly but significantly inversely associated with serum homocysteine level (r = -0.15, P = 0.04) after controlling for covariates. Soy product intake was also significantly positively correlated with serum folate (r = 0.15, P = 0.04). Although it is unclear the extent to which each component of soy, such as folate and isoflavones, is associated with the serum homocysteine concentration, this biochemical complex appears to have a favorable effect on homocysteine metabolism in premenopausal women.