OBJECTIVE To perform conventional and microdissection testicular sperm extraction (TESE) at the same session and compare their effectiveness. METHODS Prospective comparative study. METHODS University hospital setting. METHODS The study included 335 patients with nonobstructive azoospermia. METHODS Microdissection TESE was performed to 77 patient with atrophic testes. An additional 258 patients underwent conventional TESE using three incisions on three quadrants of the testis (upper, middle, and lower). Microdissection TESE was performed by enlarging the middle incision vertically when no spermatozoa could be detected using the conventional technique. METHODS Sperm retrieval, fertilization, clinical pregnancy rate (PR), and live birth rate were evaluated. The relation between sperm retrieval rate and FSH level and testis volume was also investigated. RESULTS Spermatozoa was detected in 33.7% of patients using conventional TESE. The spermatozoa detected increased to 50.8% using microdissection TESE. The increase was statistically significant. In the primary microdissection TESE group, the surgical retrieval rate was 20.8%. The overall sperm retrieval rate was 43.9%. There was a significant relation between the sperm retrieval rate and testis volume, whereas there was no relation between sperm retrieval rate and FSH levels. The overall fertilization rate, clinical PR, and live birth rate were 57.1%, 50.4%, 36.4%, respectively. CONCLUSIONS Conventional TESE combined with microdissection TESE can be used in selected patients. Sperm retrieval rate of TESE can be low in patients with atrophic testes.