Chloride/bicarbonate (Cl-/HCO(3)-) exchangers are a family of proteins (anion exchanger [AE] gene family) that regulate many vital cellular processes such as intracellular pH, cell volume, and Cl- concentration. They may also be involved in the regulation of sperm cell motility and acrosome reaction during fertilization, as these two phenomena are bicarbonate dependent, and we have previously shown that a polypeptide immunologically related to erythrocyte band 3 is expressed in mammalian sperm cells. We have now identified this putative sperm cell anion exchanger as the AE2 isoform of this gene family. First, we determined its complete primary structure from the human testis lambda gt 11 cDNA library. The cloned sequence was found to consist of 3896 base pairs (bp) with an open reading frame of 3726 bp, and to be almost identical to the previously published human genomic AE2 sequence. Only four amino acid disparities were found between these two sequences. Second, our in situ hybridization analyses showed that AE2 mRNA is expressed in developing sperm cells, indicating that the cloned sequence corresponds to the sperm cell AE. Our reverse transcription-polymerase chain reaction analyses suggested further that the expression of AE2 mRNA was variable to some extent during the epithelial cell cycle. Strongest expression was observed at stages VII-XIV except for stage X, i.e., when major structural and morphological changes take place. These results suggest that the full-length AE2 isoform regulates HCO(3)- transport in mature sperm cells and thus their motility in vivo.