PURPOSE: Microdeletions on the Y chromosome have been associated with infertile in men. The deletions cluster in three regions, named azoospermia factor (AZF): AZFa, AZFb and AZFc. It has been suggested that deletions in AZFa result in Type I Sertoli cell-only (SCO) infertility (no spermatogonia present), deletions in AZFb in spermatogenic arrest, and deletions in AZFc Type II SCO (some spermatogonia present with limited spermatogenesis). The purpose of this study was to determine the prevalence of Y chromosome microdeletions and to correlate of the pathologic presentation with specific deletions in infertile Korean men. MATERIALS AND METHODS: We analyzed 115 non-obstructive azoospermic (NOA), 30 obstructive azoospermic (OA), 30 severe oligospermic (sperm concentration <5 x 10(6)/ml) patients and 50 fathered men. We tested leukocyte DNA by PCR for the presence of STS markers, AZFa (sY84, 85, 86), AZFb (sY129, 134, 135, 143, RBM1) and AZFc (DAZ, sY242). The PCR results were confirmed by Southern hybridization and were investigated by SSCP analysis for DAZ gene muations. RESULTS: None of 30 OA and 50 fertile men had microdeletions, but 15 (13.0%) of the 115 NOA and 4 (13.3%) severely oligospermic patients had one or more microdeletions. Deletions involving only the AZFc region were found in 9 men (3 severe oligospermia, 4 spermatogenic arrest, 1 Type I SCO and 1 Type II SCO). Deletions involving only the AZFb were found in 4 (1 severe oligospermia and 3 spermatogenic arrest), and deletions involving only AZFa were found in 1 (Type I SCO). Also, deletions involving the AZFb and AZFc were found in 5 (2 severe oligospermia and 3 Type I SCO). CONCLUSIONS: The prevalence of Y chromosome microdeletion was 13.0% and 13.3% in NOA and severely oligo spermia patients. The earlier reported association with particular types of infertility was not confirmed. The region of the deletions does not correlate with severity of spermatogenic failure or the presence of visible sperm. Deletions involving more proximal regions of the Y chromosome (AZFa) seemed to be rare.