Male infertility is a common condition affecting at least 7% of men worldwide and is often genetic in origin. Using whole exome sequencing, we have identified a high confidence infertility-causing mutation in AXDND1 in a man with azoospermia. This ‘stopgain’ mutation affects the putative axonemal dynein light chain domain and is predicted to cause a complete loss of AXDND1 function. Axdnd1 is highly testis enriched in mice and men, and in male germs is largely expressed in spermatocytes and spermatids. We generated Axdnd1 knockout mice with a premature stop codon in exon 3 to further explore the role of AXDND1 in male fertility. Axdnd1 knockout mice were infertile and presented with a multifaceted phenotype that worsened with age. At 7 weeks of age, just after the first wave of spermatogenesis and epididymal maturation, spermatogenesis was intact. Normal numbers of sperm were present in the cauda epididymides of knockout males, but all were completely immotile. Electron microscopy revealed the axonemes of sperm from knockout males to be severely disrupted, with key accessory structures (outer dense fibres, microtubule doublets) missing. By 10 weeks of age there was a significant loss of germ cells in 15% of tubules, a complete loss of germ cells in 5% of tubules, and an increase in the immune cell population in the intertubular space of Axdnd1 knockout testes. This translated to a 99.3% reduction in epididymal sperm count compared to wildtype, and the presence of precociously sloughed germ cells and immune cells in the cauda epididymis. Although predicted to be an axonemal dynein protein based on the possession of an axonemal dynein light chain domain, our data suggest AXDND1 primarily plays roles in cytoplasmic dynein function in male germ cells. Specifically, we hypothesise AXDND1 is required for cargo transport during spermatogenesis, including into the developing sperm tail.