Onabotulinumtoxin A (onabotA) is gaining wide medical use in children. However, little is known about its potential testicular effects. The present study was planned to investigate the influence of its injection on the maturing testicular structures in rats. Immature rats were injected in the peritesticular area by onabotA with three doses of (10, 20 and 40 U/kg) three times in a two-week interval. The effect of these injections on fertility indices (sperm parameters, semen quality and testosterone levels) was examined. In addition, levels of antisperm antibodies and several apoptosis parameters were investigated. DNA content in form of ploidy was compared to control group via flow cytometric analysis. Histopathological examination was carried out to confirm the findings. OnabotA-injected groups showed decreased sperm count and semen quality, while sperm vitality, morphology and testosterone levels were not significantly affected. Furthermore, DNA flow cytometric analysis confirmed delayed sperm maturation. Apoptosis markers were significantly increased by the injections. In conclusion, onabotA use in growing rats adversely affected sperm count and maturation. However, it had no significant effects on sperm morphology or vitality. OnabotA testicular effects are mediated, at least partly, by apoptosis.