Recent studies suggest that genetic polymorphisms of the estrogen receptor-alpha (ER-alpha) gene may be associated with breast cancer risk. To evaluate the role of this gene in the risk of breast cancer, we genotyped a newly identified GT dinucleotide repeat [(GT)(n)] polymorphism located in the promoter region (6.6 kb upstream of the transcription start site) in 947 breast cancer cases and 993 age frequency-matched community controls from a population-based case-control study conducted among Chinese in urban Shanghai. Sixteen alleles were identified, the most common one having 16 GT repeats [(GT)(16)]. Compared with subjects homozygous for this allele, subjects carrying the (GT)(17) or (GT)(18) allele had a decreased risk of breast cancer. The odds ratios (ORs) were 0.81 [95% confidence interval (CI), 0.62-1.06] and 0.58 (95% CI, 0.36-0.94), respectively, for one and two copies of the (GT)(17) or (GT)(18) allele. The inverse association with carrying either of these alleles was stronger among women with >30 years of menstrual cycles (OR 0.66; 95% CI 0.51-0.85) than those with a shorter duration of menstrual cycles (OR 0.97; 95% CI 0.73-1.27), and the test for an interaction was statistically significant (P = 0.04). Among breast cancer patients, the presence of either the (GT)(17) or (GT)(18) allele was associated with a reduced expression of progesterone receptor. Results of this study indicate that the GT dinucleotide repeat polymorphism in ER-alpha gene promoter region may be a new biomarker for genetic susceptibility to breast cancer.