Prominin-1/CD133 is a five-membrane-span glycoprotein that is thought to act as an organizer of plasma-membrane protrusions. Here, we report the molecular and cell-biological characterization of four novel prominin-1 splice variants isolated from a mouse testis cDNA library and referred to as prominin-1.s3 to prominin-1.s6. Compared with kidney-derived prominin-1.s1, the s3, s4 and s5 variants contain a distinct cytoplasmic C-terminal domain. The s4 and s5 variants bear, in addition, two and one inframe deletion(s), respectively, in the extracellular domains. The s6 variant displays a truncated C-terminal domain caused by a premature termination resulting from intron retention. Upon their ectopic expression in Chinese hamster ovary cells, the s3 and s6 variants were found to be concentrated in plasma-membrane protrusions, whereas the s4 and s5 variants did not reach the cell surface. Biochemical analyses suggest that most of the prominin-1 in the adult male reproductive system is expressed as the s6 variant. Immunohistological and electron microscopic analyses show that prominin-1 is: (1) confined to the apical surface of the epithelium all along the epididymal duct, with the exception of the initial segment; (2) concentrated in stereocilia of the epididymal duct epithelium; and (3) found on the tail of developing spermatozoa in seminiferous tubules. Our data suggest that prominin-1 is involved in the formation and/or stabilization of epididymal stereocilia and the tail of spermatozoa, and hence might play a dual role in the biogenesis of spermatozoa.