In this paper we apply the Chip on chip approach to pursue a large scale identification of ERα-and ERβ-binding DNA regions in intact chromatin.We show that there is a high degree of overlap between the regions identified as bound by ERα and ERβ , respectively, but there are also regions that are bound by ERα only in the presence of ERβ , as well as regions that are selectively bound by either receptor.Analysis of bound regions show that regions bound by ERα have distinct properties in terms of genome landscape, sequence features and conservation compared to regions that are bound by ERβ.ERβ bound regions are, as a group, located closer to transcription start sites.ERα-and ERβ-bound regions differ in sequence properties with ERα-bound regions having an over-representation of TA-rich motifs including forkhead binding sites and ERβ-bound regions having a predominance of classical estrogen response elements (EREs) and GC-rich motifs.Differences in the properties of ER bound regions might explain some of the differences in gene expression programs and physiological effects shown by the respective ERs.