We report here on the isolation and sequencing of feline estrogen receptor alpha (ER-alpha) mRNA. Feline ER-alpha showed three alternative 5' untranslated exons and a common transcript of 6183 base pairs (bp). The putative coding sequence (1788 bp) and the unusually long 3' untranslated (3'-UTR) region (4305 bp) displayed high sequence similarity with human ER-alpha. A highly conserved sequence block was found in the 3'-UTR corresponding to a putative regulatory element for mRNA stability. In addition to wild-type ER-alpha mRNA, several exon-deleted splicing variants (ERDeltaE2, ERDeltaE3, ERDeltaE4, ERDeltaE5, ERDeltaE6, ERDeltaE7) were found in various feline tissues. This is similar to what observed in human tissues and opposite to the near absence of exon-deleted isoforms in rodents. Expression analysis of exon-deleted variants was also conducted on 24 samples of feline mammary carcinoma (FMC) and 15 normal mammary gland (NMG) controls, using a "splice targeted approach". The prevalence of some variants was similar for human and feline ER-alpha, while other isoforms were expressed at different frequencies in the two species. Two of the most frequent isoforms (ERDeltaE4, ERDeltaE7) were significantly less frequent in FMCs than in NMGs, likely as a consequence of decreased expression of ER-alpha in FMCs.