Background: Infertility is a complex condition that can originate from either male or female factors, or both. Genetic factors, such as damage to the Y chromosome, gene defects, and chromosomal anomalies significantly contribute to infertility. Consequently, cytogenetic analysis is a critical component of the systematic clinical evaluation for diagnosing, managing, and monitoring infertility. The purpose of the present study was to assess the prevalence, types, and significance of chromosomal polymorphisms in the East Indian population with a clinical history of male infertility. Methods: An investigation was conducted on 650 infertile men and 150 fertile men from general population, following the Helsinki Declaration guidelines. A cytogenetic investigation was conducted using G-banding, Ag-NOR banding, and centromeric heterochromatin staining. A Chi-square test was performed to compare the prevalence of chromosomal polymorphic variants. Results: The results of this study revealed significant chromosomal anomalies among the study population. Specifically, 2.61% of these individuals exhibited numerical chromosomal anomalies, while 1.53% showed structural chromosomal anomalies. Notably, there was a statistically significant (p<0.05) increase in the occurrence of total chromosomal polymorphic variations, with 24% of the infertile males found to have total chromosomal polymorphisms. Furthermore, the prevalence of the Yqh+ variant was statistically significant among infertile males (p=0.010), while the 9qh+ variant also showed a significant prevalence (p=0.0.35). Conclusion: The increased prevalence of chromosomal polymorphic variants underscores the need to evaluate their potential role in the etiology of male infertility.