Microdeletions of the azoospermia factor (AZF) locus on the Y chromosome have been implicated as a major genetic component of idiopathic male infertility, and the incidence of AZF deletions has been reported to be 15-20% in men with non-obstructive azoospermia (NOA). Numerous studies have described AZF deletion rates in patients with azoospermia; however, a clinical comparison of azoospermic patients with AZF deletion and those with no deletion has not been reported well. A new technique for testicular sperm extraction, microdissection testicular sperm extraction (TESE), has been used widely on NOA patients. Although testicular spermatozoa are reliably detected and retrieved from NOA patients by microdissection TESE, sperm retrieval rates for patients with AZF deletions are not well known. Therefore, characteristics of NOA patients with AZF deletion were investigated. Six of 60 patients (10%) who underwent microdissection TESE were found to have AZF deletions by genomic polymerase chain reaction. Testicular data, outcome of sperm retrieval and endocrinological profiles, were compared between patients with AZF deletions (n = 6) and those with no deletions (n = 54). Testicular size, varicocele rates and testicular histology were similar between the groups. Significant differences were not detected in the endocrinological profiles. Sperm retrieval rates were not significantly different between the groups. In conclusion, AZF deletions do not appear to confer specific characteristics to NOA patients.