Objective: This study aims to evaluate the occurrence of Y chromosome azoospermia factor (AZF) microdeletions and assess immune infertility incidence and whether there is a correlation between them. Materials and Methods: The sample included 75 infertile men who were referred to private clinics in Ramadi city as a test group and 25 healthy fertile men as a control group. The tests included analysis of seminal fluid and detection of the antibodies against the sperms at both seminal fluid and serum and diagnosed chromosomal deletions via real-time polymerase chain reactions using specific sequence-tagged sites. Results: The results reveal that 46 (61.33%) patients in the group of infertile men have AZF microdeletions, while no deletions are present in the control group. Out of the 75 infertile men, 5 patients (6.66%) from all the study groups have positive results for anti-sperm antibodies (ASA), while the others have negative results for ASA in both serum and seminal plasma. Conclusions: The prevalence of AZF microdeletions in our study population is high in Anbar Governorate of Iraq, while we find a low incidence of ASA in this study. All the patients with positive ASA results are without deletions in the Y chromosome’s AZF region. So there is no correlation between AZF microdeletion and ASA generation in infertile men in the current study.