To elucidate the impact of monogenic variants in the genes located within the Y-chromosomal AZFa region, we screened whole exome sequencing (WES) data of 1,655 well-characterized men from the Male Reproductive Genomics (MERGE) study with unexplained crypto- or azoospermia for high-impact variants in USP9Y, DDX3Y, and UTY and identified three unrelated men of European ancestry carrying different LoF variants in DDX3Y. In addition, a further LoF variant in DDX3Y was identified in WES data of the Genetics of Male Infertility Initiative (GEMINI) study25. This evidence concerns the gene USP9Y and male infertility.