Estrogen receptors (ERs) are believed to be ligand-activated transcription factors belonging to the nuclear receptor superfamily, which on ligand binding translocate into the nucleus and activate gene transcription. To date, two ERs have been identified: ERalpha and ERbeta. ERalpha plays major role in the estrogen-mediated genomic actions in both reproductive and nonreproductive tissue, whereas the function of ERbeta is still unclear. In this study, we used immunocytochemistry, immunoblotting, and proteomics to demonstrate that ERbeta localizes to the mitochondria. In immunocytochemistry studies, ERbeta was detected with two ERbeta antibodies and found to colocalize almost exclusively with a mitochondrial marker in rat primary neuron, primary cardiomyocyte, and a murine hippocampal cell line. The colocalization of ERbeta and mitochondrial markers was identified by both fluorescence and confocal microscopy. No translocation of ERbeta into the nucleus on 17beta-estradiol treatment was seen by using immunocytochemistry. Immunoblotting of purified human heart mitochondria showed an intense signal of ERbeta, whereas no signals for nuclear and other organelle markers were found. Finally, purified human heart mitochondrial proteins were separated by SDS/PAGE. The 50,000-65,000 M(r) band was digested with trypsin and subjected to matrix-assisted laser desorption/ionization mass spectrometric analysis, which revealed seven tryptic fragments that matched with those of ERbeta. In summary, this study demonstrated that ERbeta is localized to mitochondria, suggesting a role for mitochondrial ERbeta in estrogen effects on this important organelle.