Estrogen-related receptor ␣ (ERR␣) is an orphan member of the superfamily of nuclear hormone receptors. ERR␣ was initially isolated based on its sequence homology to the estrogen receptor but is not activated by classic estrogens. To identify possible physiologic functions for this orphan receptor, we cloned the mouse ERR␣ cDNA and used it to characterize the expression of ERR␣ transcripts and to identify potential ERR␣ target genes. RNA in situ hybridization studies detect ERR␣ transcripts in an organ-specific manner through mid-to late embryonic development, with persistent high-level expression in brown adipose tissue and intestinal mucosa. In the adult mouse, ERR␣ is most highly expressed in kidney, heart, and brown adipocytes, tissues which preferentially metabolize fatty acids. Binding site selection experiments show that ERR␣ preferentially binds to an ERR␣ response element ( The orphan nuclear receptor estrogen-related receptor ␣ (ERR␣) was initially cloned by low-stringency screening of a human kidney library with an estrogen receptor DNA binding domain probe (12). Subsequently, protein micropurification and microsequencing techniques identified ERR␣ as a repressor of the simian virus 40 major late promoter and implicated the receptor as a key regulator of the early-to-late switch of simian virus 40 gene expression (35). ERR␣ has also been shown to accentuate estrogen-dependent induction of the complex lactoferrin estrogen response element (ERE), possibly by forming heterodimers with the estrogen receptor (39). While ERR␣ displays significant homology to the estrogen receptor, it does not bind estrogens in vitro, nor is its transcriptional activity modulated by estrogens (12, 39). Like many other members of the nuclear receptor superfamily, ERR␣ has no known ligand and is therefore considered an orphan receptor. In the absence of an associated ligand, one approach to uncovering potential physiologic roles for ERR␣ is to identify possible target genes.