summary Detection of Y-chromosome microdeletion is useful to obtain reliable genetic information for assisted reproductive techniques, thus avoiding unnecessary treatment and vertical transmission of genetic defects. Purposes This research was conducted over a six-year period to analyze clinical data, somatic cytogenetic abnormalities, and types of microdeletions in men with fertility disorders in Iran. Methods and Patients A total of 3654 infertile men were included in this study. Semen samples were analyzed according to standard methods. Conventional chromosomal karyotyping was used to analyze chromosome abnormalities.Polymerase chain reaction (PCR) amplification using nine specific sequence-tagged sites (STS) was used to detect AZF microdeletions. Results Out of the 3654 patients who were analyzed, AZF region microdeletions were detected in 185 cases (5.06 %). Karyotype analysis was available for 157 men and among them abnormal karyotypes were found in 51 cases (32.48 %). One hundred and forty-seven cases with Yq microdeletions suffered from azoospermia and 38 from severe oligozoospermia. Our data show that the most frequent microdeletions were in the AZFc region, followed by the AZFb+c+d, AZFb+c, AZFb, AZFa, and AZF a+c regions. Conclusion The study has confirmed that the detection of microdeletions in the AZF region is significant from a diagnostic viewpoint. It is also useful to obtain reliable genetic information from infertile men to determine the etiology of the deletions, and to avoid unnecessary treatments and vertical transmission of genetic defects.