Tamoxifen, a small-molecule antagonist of the transcription factor estrogen receptor alpha (ERa) used to treat breast cancer, increases risks of endometrial cancer. However, no parallels of ERa transcriptional action in breast and endometrial tumors have been found that might explain this effect. In this study, we addressed this issue with a genome-wide assessment of ERa-chromatin interactions in surgical specimens obtained from patients with tamoxifen-associated endometrial cancer. ERa was found at active enhancers in endometrial cancer cells as marked by the presence of RNA polymerase II and the histone marker H3K27Ac. These ERa binding sites were highly conserved between breast and endometrial cancer and enriched in binding motifs for the transcription factor FOXA1, which displayed substantial overlap with ERa binding sites proximal to genes involved in classical ERa target genes.Multifactorial ChIP-seq data integration from the endometrial cancer cell line Ishikawa illustrated a functional genomic network involving ERa and FOXA1 together with the enhancerenriched transcriptional regulators p300, FOXM1, TEAD4, FNFIC, CEBP8, and TCF12. Immunohistochemical analysis of 230 primary endometrial tumor specimens showed that lack of FOXA1 and ERa expression was associated with a longer interval between breast cancer and the emergence of endometrial cancer, exclusively in tamoxifen-treated patients. Our results define conserved sites for a genomic interplay between FOXA1 and ERa in breast cancer and tamoxifen-associated endometrial cancer. In addition, FOXA1 and ERa are associated with the interval time between breast cancer and endometrial cancer only in tamoxifen-treated breast cancer patients. Cancer Res; 76(13); 3773-84. Ó2016 AACR.