Estrogen Receptor alpha (ER) is the key driver in the majority of all breast cancers, and considered the main target for therapy. However, resistance to treatment is common and biomarkers to facilitate optimal treatment selection are urgently needed. Even though the vast majority of breast cancer patients are female, breast cancer can develop in men as well. Using chromatin immunoprecipitation followed by massive-parallel sequencing (ChIP-seq), we identified the genome-wide chromatin binding profiles of ER in male and female breast tissue, which we compared with profiles found in cell lines. Interestingly, while in cell lines only ~5% of ER chromatin binding sites are observed at promoter regions, a substantially higher promoter-occupancy of ER was found in tumor tissue from both sexes. By assessing inter-tumor heterogeneity of ER chromatin binding sites, a stronger conservation of promoter-binding by ER was found as compared to enhancer regions, which was directly compared with enhancer activity analyses in healthy breast tissue. By integrating both common and unique ER-bound enhancers with somatic mutation data and breast cancer risk SNPs, we aim to identify whether diversity of enhancer action and ER genomic selectivity between tumors may represent a driving factor in tumor development and progression.