Estrogens play a key role in bone structural integrity, which is maintained by the opposing activity of bone forming osteoblasts and bone resorbing osteoclasts. The cellular effects of estrogens are mediated by estrogen receptors, however, the detailed molecular mechanism of ER regulation in osteoclasts has not yet been elucidated. We provide here a detailed analysis of the expression profile and functionality of ER during osteoclast differentiation. We employed a human primary osteoclast cell culture model to evaluate the regulation of estrogen receptor (ER) variant expression. We characterized the expression profile of estrogen receptors and studied the regulation of the predominant estrogen receptor-alpha (ER-alpha) during differentiation into osteoclasts. In addition to the full-length ER-alpha, a shorter ER-alpha mRNA variant is expressed and both ER-alpha variants are regulated during osteoclastogenesis. Furthermore, we show that the pS2 gene is an estrogen-regulated gene in osteoclasts. Analysis of the activity of the pS2 gene throughout differentiation, using chromatin immunoprecipitation (ChIP), revealed the functionality of ER-alpha during differentiation and shows that the occupancy of ER-alpha and activated polymerase II on the pS2 promoter decrease with time and can be blocked by the ER antagonist ICI 182780. These results help to dissect the molecular events relevant to estrogen signaling and provide a better understanding of the role of ER-alpha regulation during bone resorption mediated by osteoclasts.