To systematically investigate the genetic architecture of severe male infertility in Indian men, with a specific focus on chromosomal abnormalities and the contribution of de novo variants.We recruited 247 infertile males between 2021 and 2024 presenting with severe quantitative and qualitative sperm defects. All patients underwent karyotyping and Y chromosome microdeletion STS-PCR. A single molecule molecular inversion probe-based targeted sequencing assay covering 39 male infertility genes was performed in 120 patients, while whole exome sequencing (WES) was conducted in 48 patients using a duo/trio-based approach to enable segregation and de novo variant detection.Gonosomal aneuploidies were observed in 3/247 patients (1.2%, 95% CI 0.3-3.5%) and causal AZF microdeletions in 8/247 (3.2%, 95% CI 1.4-6.3%). Targeted sequencing identified pathogenic/likely pathogenic (P/LP) variants in 4/120 patients (3.3%, 95% CI 0.9-8.3%), with additional CFTR variants in 3 patients where parental DNA was unavailable for phasing. WES yielded P/LP variants in 4/48 patients (8.3%, 95% CI 2.3-19.9%) affecting PMFBP1, DNAH1, and AR genes, confirmed via segregation analysis. No de novo or copy number variants were confirmed as causative, though several candidate genes were prioritised. Sequencing-based approaches provided an additional ~ 6-8% diagnostic yield, with the overall diagnostic rate reaching 7.7% (19/247; 95% CI 4.7-11.8%).Sequencing-based strategies, particularly family-based trio WES, significantly enhance diagnostic yield beyond current guideline-recommended tests, with data supporting their adoption as first-tier investigations for severe male infertility. This represents India's largest cohort-based genomic study on male infertility to date. Larger family-based cohorts will be essential to delineate the contribution of de novo variants to male infertility genetics.