The existence of two forms of the chicken estrogen receptor-alpha protein (ER-alpha) in chicken tissues is demonstrated: the previously reported receptor (cER-alpha form I), which has a size of 66 kDa, and a new form (cER-alpha form II), which lacks the N-terminal 41 amino acids present in form I and thus gives rise to a protein of 61 kDa. Whereas the 66-kDa protein is the translation product of several cER-alpha mRNAs (A1-D), the cER-alpha protein isoform II is encoded by a new cER-alpha mRNA (A2), which is transcribed in vivo from a specific promoter that is located in the region of the previously assigned translation start site of the cER-alpha gene. SI nuclease mapping analysis reveals that cER-alpha mRNA A2 is liver enriched. The resulting cER-alpha forms I and II differ in their ability to modulate estrogen target gene expression in a promoter- and cell type-specific manner. Whereas cER-alpha form I activates or represses in a strictly E2-dependent manner, the truncated form is characterized by a partial transactivating or repressing activity in the absence of its ligand. Comparison of the N-terminal coding regions of different vertebrate ER-alpha reveal a conservation of the translation start methionine of the protein ER-alpha form II in other oviparous species but not in mammals. The expression of two classes of ER-alpha transcripts encoding the two ER-alpha receptor forms in the liver of Xenopus laevis and rainbow trout is demonstrated. Therefore, the existence of two functionally different protein isoforms produced from the ER-alpha gene is probably a common and specific feature in oviparous species.