Abstract: A case-control study was conducted to establish a database of ESR1 polymorphisms in Iranian population in order to compare Western and Iranian (Middle East) distributions and to evaluate ESR1 polymorphism as an indicator of clinical outcome. The ESR1 gene was scanned in Iranian patients newly diagnosed invasive breast tumors, (150 patients) and in healthy individuals (147 healthy control individuals). PCR single-strand conformation polymorphism technology and direct sequencing was performed. The silent single nucleotide polymorphism (SNPs) was found, as reported previously in other studies, but at significantly different frequencies. The frequency of genotype 01 in codon 594 (ACG→ACA), (G3242A), exon 8 was significantly higher in breast cancer patients (48.0%) than in control individuals (1.4%; p = 0.001). The allele 1 in codon 594 was significantly more common in breast cancer patients with age at menarche ESR1 genotype, as determined during pre-surgical evaluation, might represent a surrogate marker to increase predicting breast cancer in Iranian population.