Side effects of ciprofloxacin (CPFX), a widely used broad spectrum antibiotic with fluoroquinolone core, have been reported in different organs. In the present study we sought to elucidate the impact of ciprofloxacin on sperm chromatin integrity and sperm DNA damage using Aniline Blue and Acridine Orange technique, respectively. The fertility potential in male mice was also evaluated. NMRI male mice of 8-week old were included in this study and they were randomly divided into three groups. The first group was received low dose (LD) of ciprofloxacin (206 mg kg-1, PO) and the second was treated with high dose (HD) of ciprofloxacin (412 mg kg-1, PO) for 45 consecutive days. The control mice were only treated with oral carboxymethyl cellulose for 45 consecutive days. Sperm cells were removed from cauda epididymis and analyzed for chromatin integrity and DNA damage. In addition, the rate of fertilization, two cell embryos, blastocysts, arrested embryos and their types was examined using zygotes cultured in human tubal fluid - bovine serum albumin (HTF-BSA) medium. Concomitant significant increase in DNA damage and protamine deficiency of the sperm cells in ciprofloxacin treated mice were observed (P < 0.05). In addition, the fertilization rate and embryonic development in treated mice were significantly lower than that of control mice, but the embryo arrest rate in treated mice was significantly higher than that of control group (P < 0.001). In conclusion CPFX was able to induce DNA damage and chromatin abnormalities of sperm cells which could be contributed in the observed low fertilization rate and retarded embryonic development.