Deletion of specific genes present in the long arm of Y chromosome has been identified as the most common genetic cause of defective spermatogenesis. Studies have shown that frequency of Y chromosome microdeletion varies in different geographical location and is related to genetic and environmental influence preponderance. Therefore, the present study was carried out to identify the frequency of Y chromosome microdeletion in the northern region of India and to define subgroup of infertile patients who are critically under more risk of having microdeletion. A total of 292 north Indian infertile males with nonobstructive azoospermia and oligozoospermia were selected for screening the Y chromosome microdeletion. Healthy fertile males (n=100) were also enrolled as control subjects. Frequency of Y chromosome microdeletion in north Indian infertile males was found to be about 8.5%, with azoospermia factor (AZFc) region as the most susceptible region for microdeletion. Comparatively microdeletion is more common in patients with nonobstructive azoospermia thanoligozoospermia (9.2% versus 7.1%). Statistical analysis also revealed that patients with hormonal FSH level between 20 and 40 mIU/mL have more chances of harbouring microdeletion. Hence, the present study highlights the importance of screening AZFc region among infertile patients with very high serum FSH value.