Male infertility is a common condition affecting at least 7% of men worldwide and is often genetic in origin. Using exome sequencing, we have identified an infertility-causing mutation in AXDND1 in a man with azoospermia. This ‘stop-gain’ mutation affects the axonemal dynein domain and causes a complete loss of AXDND1 function. Axdnd1 is highly testis enriched in mammals, 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 and knockout males interestingly generated 30% additional sperm compared to wild type. However, sperm collected from the cauda epididymides of knockout males were completely immotile and morphologically abnormal. Electron microscopy revealed the sperm axoneme to be severely disrupted, with key accessory structures such as outer dense fibres missing. By 10 weeks of age there was a significant loss of germ cells was observed, in concert with an increase in the immune cell population in the intertubular space of Axdnd1 knockout testes. The loss of germ cells worsened with age and by 6 months only 20% of tubules presented with intact spermatogenesis. This translated to a 99.3% reduction in epididymal sperm count compared to wild type, and the presence of precociously sloughed germ cells and immune cells in the cauda epididymis. Although classified as an axonemal dynein protein that plays roles in axoneme function, 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.