Globally it is estimated that about 15-20% of couples are affected by infertility current data from the literature show that in 50% of cases the male causal factor is involved. Genetic abnormalities cause 15%–30% of male factor infertility. Y microdeletion and CFTR gene mutations are the most frequent known molecular genetic causes associated with azoospermia and severe oligozoospermia. The purpose of the study was to evaluate genetic markers of Y-chromosome microdeletions of the AZF and cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations in azoospermic infertile men. The study was carried out on infertile men with azoospermia recruited among infertile couples referred for reproductive treatment. All patients signed an informed consent. The endocrine markers: FSH (Follicle-stimulating hormone); LH (Luteinizing Hormone); and testosterone were evaluated. They were investigated by molecular testing for AZF and CFTR gene. Multiplex Polymerase chain reaction (PCR) was performed using Y-specific markers for AZF region: AZFa (sY84, sY86, DBY1, sY620), AZFb (sY117, sY127, sY134, SY143), and AZFc (sY254, sY255, sY153, SY158). The detections of sY14 (SRY) and ZFX/ZFY were employed as internal controls. Two common mutations ΔF508 and G542X were tested of the CFTR gene. Deletions of Y chromosome were identified in 9 (9,9%) of 91 patients with azoospermia. Deletions of AZFc - sY153, sY158, sY254 and sY255 locus were observed in four of nine azoospermic patients 55,5%. In two (22,2%) patients were detected with deletion of AZFb region, deleted markers were sY117, sY127, sY134, sY143. Deletions affecting both AZFb and AZFc loci were found in two patients 22,2%. The average level of FSH was 6,4 ±3,5, LH 6,2 ±3,2 and testosterone 3,3 ±1,4, of patients with microdeletions. Three (3,3%) patients were identified with CFTR gene mutation ΔF508, for calculating the risk of recurrence in offspring was investigated and his wife, found himself homozygous. Molecular genetic screening is important to define the cause of spermatogenesis defect. This is important to provide a correct diagnosis and more effective solutions to couples with infertility before reproduction treatment is applied.