Background: Ciprofloxacin is a commonly prescribed antibiotic in the treatment of genitourinary tract infection. Objective: The aim of this study was to investigate the effects of ciprofloxacin on testis apoptosis and sperm parameters in rat. Materials and Methods: Twenty male Wistar rats were selected and randomly divided into two groups; control (n=10) and experimental (n=10). The experimental group was orally received 12.5 mg/kg ciprofloxacin daily for 60 days and the control group just received water and food. Rats were then killed and sperm removed from cauda epididymis and analyzed for sperm motility, morphology, and viability. Testis tissues were also removed and prepared for TUNEL assay to detect apoptosis. Results: Results showed that ciprofloxacin significantly decreased the sperm concentration, motility (p<0.05) and viability (p<0.001). In addition, ciprofloxacin treatment resulted in a significant decrease in the number of spermatogenic cells (spermatogonia, spermatocyte, spermatid and sperm) in the seminiferous tubules when compared with the control group. The apoptotic germ cells per seminiferous tubular cross section was significantly increased in the experimental group (15.11±3.523) as compared with the control group (7.3±0.762) (p<0.05). Conclusion: It is concluded that ciprofloxacin has the toxicological effects on reproductive system in male rats.