AbstractBackgroundGenetic causes that lead to spermatogenetic failure in patients with nonobstructive azoospermia (NOA) have not been yet completely established.ObjectiveTo identify low‐frequency NOA‐associated single nucleotide variants (SNVs) using whole‐genome sequencing (WGS).Materials and methodsMen with various types of NOA (n= 39), including samples that had been previously tested with whole‐exome sequencing (WES;n= 6) and did not result in diagnostic conclusions. Variants were annotated using the Ensembl Variant Effect Predictor, utilizing frequencies from GnomAD and other databases to provide clinically relevant information (ClinVar), conservation scores (phyloP), and effect predictions (i.e., MutationTaster). Structural protein modeling was also performed.ResultsUsing WGS, we revealed potential NOA‐associated SNVs, such as:TKTL1, IGSF1, ZFPM2, VCX3A(novel disease causing variants),ESX1, TEX13A, TEX14, DNAH1, FANCM, QRICH2, FSIP2, USP9Y, PMFBP1, MEI1, PIWIL1, WDR66, ZFX, KCND1, KIAA1210, DHRSX, ZMYM3, FAM47C, FANCB, FAM50B(genes previously known to be associated with infertility) andALG13, BEND2, BRWD3, DDX53, TAF4, FAM47B, FAM9B, FAM9C, MAGEB6, MAP3K15, RBMXL3, SSX3andFMR1NBgenes, which may be involved in spermatogenesis.Discussion and conclusionIn this study, we identified novel potential candidate NOA‐associated genes in 29 individuals out of 39 azoospermic males. Note that in 5 out of 6 patients subjected previously to WES analysis, which did not disclose potentially causative variants, the WGS analysis was successful with NOA‐associated gene findings.