Abstract : Context: Y chromosome microdeletions in infertile men of Tamil Nadu, South India. Aim: The paper assesses the association of Y chromosome microdeletions among infertile patients using several STS markers from each AZF (AZoospermic Factor) region and also aspires to determine whether the blood DNA microdeletion picture matches the semen DNA Yq microdeletion map. Materials and Methods: A total of 287 men, including 147 infertile men and 140 normozoospermic fertile controls were included for the study. Results: Screening 72 semen samples with the STS markers specific to AZF (a,b,c) regions showed Y chromosome microdeletions in 19 (12.9%) individuals. No deletion was observed in all the three AZF regions by screening 45 blood and 30 paired samples. None of the control men showed deletion for the 28 STS markers, which were used for the primary screening of the deletion of AZF a,b,c regions. Conclusion: Germ cell DNA can be analyzed for Yq microdeletions rather than blood DNA.