Spermatogenesis is critically dependent on several complex microtubule structures including the meiotic spindle, the spermatid manchette and the axoneme of the sperm flagellum. Despite this, the microtubule regulatory machinery of testicular cells is largely unexplored and constitutes a potentially novel avenue in understanding many causes of male infertility. The eponymous microtubule-severing enzyme, Katanin, is a heterodimer consisting of a severing enzyme subunit, KATNA1 (p60), and an associated regulatory subunit, KATNB1 (p80). This complex acts to regulate both microtubule number and length and is proving to be especially important in the generation of male gametes. Recent work has revealed that a mutation in the p80 subunit causes sterility in male mice due to disturbances in the microtubule structures of the developing germ cells1. Two vertebrate specific homologs of katanin p60 are also highly enriched in the testis, suggesting that individual katanin enzymes may differentially regulate different aspects of spermatogenesis. Indeed, mutation in one homolog, Katnal1, causes male sterility and, in contrast to p80 mutation, microtubule disruption is largely restricted to Sertoli cells2. Here we have shown that the previously uncharacterised p60 homolog, KATNAL2, is also essential for male fertility. Both a point mutation and complete knockdown of Kantal2 in mice resulted in impaired differentiation of spermatids into spermatozoa and a complete retention of sperm in the seminiferous epithelium. In the absence of KATNAL2, abnormal multiplication of the basal body was observed in spermatids followed by an absence of flagellum generation in later steps. Concomitantly, spermatids exhibited defects in head shaping. Overall our findings suggest KATNAL2 is essential for the latter steps of spermatogenesis supporting the premise that a series of katanin proteins are utilised to provide differential regulation of the various microtubule structures in developing germ cells.