We investigated the association between dinucleotide (thymine-adenine) repeat polymorphism lying upstream of human estrogen receptor (ER) gene and bone mineral density (BMD) as well as biochemical markers for bone metabolism in 144 healthy postmenopausal Japanese women. The genotype was classified into 'A' through 'R' according to the number of the repeats, from 10 to 27. BMD was expressed in Z score (a deviation from the weight-adjusted average BMD of each age using the standard deviation as a unit). The people having genotype C (12 repeats of thymine-adenine) allele (n = 15) had significantly lower Z score of spine BMD (mean +/- SD; -1.11 +/- 1.3 vs. -0.06 +/- 1.2; p < 0.01) and of total body BMD (-0.58 +/- 1.0 vs. 0.31 +/- 0.9; p < 0.01) than those without this genotype (n = 129). They also had significantly higher levels of serum intact osteocalcin, urinary pyridinoline, and urinary deoxypyridinoline. These results suggest that genetic variation at the ER locus may be associated with some determinants for BMD and bone metabolism in postmenopausal women.