Sodium-hydrogen exchanger as a channel for regulation of intracellular pH might be a crucial modulator of sperm capacitation and motility. Three members of this family have been identified in spermatozoa. A novel protein testis-specific sodium-hydrogen exchanger named mtsNHE was cloned in the present study. The mtsNHE localizing on principle piece of sperm flagellum contained 12 predicted transmembrane regions without cytoplasmic fragment at carboxyl terminus. Hydrophilic region was common in the sodium-hydrogen exchanger family members. Polyclonal antibodies to trans-membrane region significantly reduced sperm motility, acrosome reaction and ratio of in vitro fertilization. By in-pouring the antibodies in sperm solution, intracellular pH and calcium concentration were decreased. Muscle injection of female mice with the specific gene vaccine of mtsNHE, significantly stepped down fertility rate. Considering its specific expression and involvement in the regulation of fertility, the mtsNHE might be a potential target molecule for developing a new male contraceptive.