Objective To investigate the condition of microdeletions of AZF region of the Y chromosome in Chinese patients with spermatogenetic malfunction. Methods Six Y chromosome specific sequence-tagged-sites(STS) in AZF region were screened and the microdeletions were determined by PCR in 27 patients with spermatogenetic malfunction. Results Microdeletions in genomic DNA were observed in 2 cases who presented with azoospermia and limited to AZFc subregion.The total deletion rate was 7.4%.The deletion patterns of the 2 cases were DAZ(sY254,sY255) and DAZ plus sY157,respectively. Conclusions Like other races, microdeletions of the Y chromosome in Chinese people may be one of the causes of spermatogenetic malfunction.Therefore prior to assistant reproduction,screening for microdeletions of the Y chromosome in patients with spermatogenetic malfunction is necessary.