OBJECTIVE To study the sperm deoxyribonucleic acid (DNA) fragmentation index (DFI), testicular volume, semen parameters, and hormone profile in human chorionic gonadotropin (hCG)- and human menopausal gonadotrophin (hMG)-treated patients with hypogonadotropic hypogonadism (HH) with and without a successful pregnancy. METHODS This is a cross sectional study. The study initially included 81 patients with HH and azoospermia at the Infertility Unit of Royan Institute between 2010 and 2012. Fifty-eight of 81 patients achieved >1 × 10(6) sperm/mL during hCG and hMG therapy. These 58 patients were divided into the following 2 groups: 20 patients with HH who achieved pregnancy in response to hCG/hMG (responders, 16 naturally and 4 by intrauterine insemination) and 38 gonadotropin-treated patients with HH with failed pregnancy (nonresponders, 29 naturally, 5 by intrauterine insemination, 1 by in vitro fertilization, and 3 by intracytoplasmic sperm injection). Sperm DNA fragmentation was visualized by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay. RESULTS Average of DFI (responders: 13.45 ± 0.64; nonresponders: 21.92 ± 0.86), age, body mass index, testis volume semen parameters, and follicle-stimulating hormone, luteinizing hormone, and testosterone levels in the 2 groups were calculated. Cut-off point for DFI was determined by receiver operating curve analysis (17.5%). CONCLUSIONS It was shown that DFI in responders is significantly lower than DFI in nonresponders (P <.001), and duration of hCG and hMG therapy in responders is significantly higher than those of nonresponders (P <.05). DFI could be predictive of conception (P <.001; odds ratio 0.57; 95% confidence interval 0.417-0.778). It can be concluded that despite low sperm quality, especially sperm concentration in these patients, decreasing sperm DNA damage may result in successful fertilization.