Polymorphisms in estrogen receptor alpha gene (ESR1) have been previously associated with breast cancer risk; however, the results were not fully consistent. Our purpose was to study interactions between common genotypes in ESR1, breast cancer risk and tumor phenotypes. 6 ESR1 single nucleotide polymorphisms (SNPs) were genotyped in 103 breast cancer patients and 90 controls using hybridization probes; the genotypes were correlated with known prognostic factors for breast cancer and 5 years-follow up data. To assess estrogen and progesterone receptors (ER, PR) and HER2/neu expressions, immunohistochemistry was performed. Our results showed that rs3798577 was significantly associated with the risk of breast cancer, the common allele C conferring susceptibility (p-trend=4 x 10(-5)); rs3798577 was also correlated with PR expression (p=0.01), but not with ER expression; rs2228480 (p=0.047) and rs1801132 (p=0.02) were associated with the age at diagnosis; rs1801132 was correlated with hypercholesterolemia (p=0.003) and increased BMI (body mass index) (p=0.01); rs2234693 showed a low significant association (p=0.042) with the tumor grade; rs3798577 was correlated with disease-free survival (p=0.05), allele C conferring increased risk for relapses, but it reached not statistical significance after adjustments. In conclusions, we identified four genotypes significantly correlated with either the risk or some tumor characteristics, suggesting that the main selection criteria of the investigated SNPs (frequency and the position in modulating domains of the gene) are pertinent instruments for establish correlations between the gene structure and the tumor phenotype.