Genetic factors cause about 15% of male infertility and microdeletions of Y chromosome is one of the genetic causes in idiopathic infertile men. Azoospermia factors (AZFa, AZFb, and AZFc) on Yq long arm are most important for spermatogenesis. For analysis of microdeletions in the AZF regions by sequence-tagged-site (STS) PCR is important screening method for infertility. An attempt has been made to evaluate the frequencies of microdeletions of AZFa, AZFb, AZFc in idiopathic cases of azoospermic and oligozoospermic subjects. Total 160 subjects (90 oligozoospermia and 70 azoospermia) and 50 control subjects were analyzed in this study. DNA samples were analyzed for microdeletions of Y chromosome by PCR-screening of 18 STS markers from different locus of the AZFa, AZFb, AZFc on Yq and SRY on Yp. The semen analysis was done and infertile men showing normal karyotype only were included in the study. Plasma follicle stimulating hormone (FSH) and leutinizating hormone concentrations were determined to rule out hormonal abnormality. Out of 160 analyzed cases, 17 (10.6%) subjects showed partial deletion of AZF regions, of which deletion in AZFc region was the most common (58.8%) and it was followed by AZFb and AZFa. The four subjects were shown two or more STS primer deleted sites and overall frequency of Y chromosome microdeletion in our subjects is 10.6%. The sites and sizes of deletions varied among patients. No deletions observed in control subjects. The varied frequencies of Y microdeletions are reported in infertile men in Indian population. From the results of this study it can be suggest that the frequency of deletions may be affected by study sample size, selection criteria of subjects and different geographical region. So, the screening of Y microdeletions is necessary along with the chromosomal analysis in case of infertile men.