Estrogen receptors exist in many cellular pools throughout most organs. This is true for the alpha and beta isoforms that are responsible for the actions of the sex steroid on normal organ development and function, and both opposing and promoting organ pathophysiology. Although many additional proteins have been speculated to act as estrogen receptors, scant evidence supports this role. In contrast, classical ERα and ERβ are found in multiple cellular pools, and only the complete knockout of these receptors produces a profound series of phenotypes that define the important functions of these sex steroid receptors. However, total deletion of the classical receptors does not inform us of the contributions of each cellular pool. We therefore have made transgenic mice, representing the selective loss of the nuclear receptor pool (membrane-only ERalpha (MOER) mice) or loss of the membrane pool (nuclear-only,NOER) mice. Using these mice, we have defined unique phenotypes, novel gene regulatory mechanisms, and metabolic signatures. For most complex organ development and biological functions, both membrane and nuclear ERα are generally required but in specific ways.