We have identified and characterized a novel human estrogen receptor (ER) beta isoform, ER beta cx, which is truncated at the C-terminal region but has an extra 26 amino acids due to alternative splicing. The ER beta cx transcript is expressed in testis, ovary, thymus and prostate as well as in human cultured cell lines such as HEC-1, HOS-TE85 and Saos-2 cells. ER beta cx protein is also immunodetectable in these human cells. Biochemical analysis reveals that the average dissociation constants (K-d) of ER alpha and ER beta for 17 beta-estradiol (E-2) are 0.2 and 0.6 nM respectively, but ER beta cx has no ligand binding ability. ER alpha and ER beta proteins bind to the estrogen response element, whereas ER beta cx does not form any shifted complex in gel shift assays. In a transient expression assay, ER beta cx shows no ligand-dependent transactivation ability of a basal promoter and also cannot interact with a cofactor, TIFl alpha, in the presence or absence of E-2. ER beta cx preferentially forms a heterodimer with ER alpha rather than that with ER beta, inhibiting DNA binding by ER alpha. Interestingly however, it shows a significant dominant negative activity only against ER alpha transactivation. Thus, this study indicates that ER beta cx potentially inhibits ER alpha-mediated estrogen action and that alternative splicing of the C-terminal region and its inhibitory properties are characteristic of several members of nuclear receptor isoforms.