Nutritional interventions targeting homocysteine remain controversial, and further nutritional research is warranted. We thus sought to explore the determinants of plasma homocysteine other than B-group vitamins. This cross-sectional study surveyed the nutritional status of 713 Japanese postmenopausal women using a semiquantitative food frequency questionnaire. Associations between total energy, protein, fat, carbohydrate, and vitamin A and K intakes and homocysteine were insignificant. Mean homocysteine in the second (536.1 ± 34.7 mg/day) and third (712.9 ± 115.6 mg/day) tertiles of calcium intake were lower than in the first tertile (379.6 ± 76.6 mg/day) by −0.57 nmol/mL (95 % confidence interval, −1.10 to −0.04, p = 0.04) and −1.18 nmol/mL (−1.76 to −0.60, p < 0.01), respectively, after adjustment for lifestyle and clinical factors (trend p < 0.01). Mean homocysteine in those with dietary calcium intake above the median (>536 mg/day) were lower regardless of the folic acid concentration; the differences were −1.59 nmol/mL (−2.33 to −0.85, p = 0.02) and −0.75 nmol/mL (−1.37 to −0.12, p < 0.01) for the high (<7.8 ng/mL) and low folic acid groups, respectively. There was no significant association between calcium and folic acid (p = 0.08). In conclusion, further prospective research to confirm our findings is needed for the development of nutritional inventions targeting homocysteine.