Objective To explore the relationship between Y chromosomal microdeletions and chromosome karyotype,clinical phenotypes and sex hormone levels in patients with spermatogenic failure.Methods SRY gene,ZFY gene and 6 sequence-tagged-sites in AZFa,AZFb and AZFc were detected with multiplex polymerase chain reaction in 42 non-obstructive azoospermic and 39 severe oligozoospermic men.Results Ten cases (12.35%) of microdeletions were found in 81 non-obstructive azoospermic (6 cases) or severe oligozoospermic patients (4 cases).Among the 10 patients with Y chromosomal microdeletions, 1 had deletion of AZFa+AZFb+AZFc,2 AZFb+AZFc, 1 AZFb and 6 AZFc.Conclusion Microdeletions in the long arm of Y chromosome were associated with spermatogenic failure.Screening for Y chromosomal microdeletions in azoospermic or severe oligozoospermic patients should be of necessity and significance.