OBJECTIVE: To determine the efficacy of topical 0.3% ciprofloxacin in reducing conjunctival biota in patients undergoing cataract surgery. PATIENTS AND METHODS: Experimental, prospective, randomized, controlled and single-blind study. Forty-six eyes of 46 patients were randomized into 2 groups, the study group (n=23) received topical 0.3% ciprofloxacin one day before surgery for six times, and on the day of the surgery one drop every 15minutes starting one hour before surgery until 3 doses were completed. The control group (n=23) did not receive any antibiotics. For both groups for the surgical field 10% povidone-iodine was applied. Samples from the conjunctiva were taken at four different times and then cultured on solid media (chocolate agar, blood agar) and enrichment broth (thioglycolate). The aqueous humor samples were also cultured in thioglycolate. The presence of bacteria was identified quantitatively and qualitatively, and the frequency of contamination was measured by considering the presence of bacteria in liquid and solid culture media. The number of colony forming units (CFU) was counted in the solid culture medium. RESULTS: Positive cultures were obtained in 82.6% and 78.2% of the patients in the study and control groups, respectively, before the administration of 0.3% ciprofloxacin. The administration of 0.3% ciprofloxacin significantly reduced the CFU compared to the control group (P<.05). Immediately after the use of povidone-iodine, the proportion of patients with a positive culture decreased to 21.7% in the study group, and 8.7% in the control group. At the end of the surgery, this percentage was 26% and 30.4%, respectively. The most common isolated pathogen was negative-coagulase Staphylococcus (66.7%). CONCLUSION: The administration of 0.3% ciprofloxacin reduces conjunctival bacterial load in the preoperative period. However, it was unable to eradicate the bacteria completely. The administration of povidone-iodine reduced conjunctival biota in 50%-70% of patients undergoing cataract surgery.