Topical antibacterial agents, used as an off-label indication, are frequently administered pre- and postoperatively to prevent endophthalmitis. We compared topical treatment with fluoroquinolone (FQ) anti-infectives to non-FQ antibacterial agents to prevent Staphylococcus aureus endophthalmitis. We hypothesize that FQ anti-infectives are more effective than non-FQ antibacterial agents for preventing endophthalmitis. Moxifloxacin 0.5%, ofloxacin 0.3%, gentamicin 0.3%, chloramphenicol 0.5%, polymyxin B/trimethoprim (10,000 units/mL/0.1%), povidone-iodine 5%, and saline were tested for topical treatment to prevent endophthalmitis. Topical treatment was applied every 15 min for 1 h (5 drops) to the left eye of 14 rabbits for each antibacterial agent and saline. After appropriate anesthesia, the anterior chambers were injected with 1×10(5) colony-forming units of a clinical endophthalmitis isolate of a S. aureus that was susceptible to all tested antibacterials. One drop was administered immediately and another 4 drops of topical treatment were applied over 24 h after injection. At 24 h postinjection, the eyes were graded for clinical signs of endophthalmitis (ocular discharge, conjunctivitis/scleral injection, limbal injection, hypopyon*, iritis*, anterior chamber cells*, anterior chamber flare*, corneal infiltration, and fibrin production*) using a severity scale (0-3). The indication of clinical endophthalmitis was a total score of >3.0 for the presentations marked with an asterisk. The data were analyzed using Fisher's Exact Randomization or Mann-Whitney nonparametric testing. Topical ofloxacin (14/14, 100% without endophthalmitis) and moxifloxacin (13/14, 93%) prevented the clinical presentation of endophthalmitis significantly more frequently (P=0.03, Fisher's Exact Test (FE)) than topical gentamicin (7/14, 50%), povidone iodine (4/14, 29%), chloramphenicol (0/14, 0%), polymyxin B/trimethoprim (0/14, 0%), and saline (0/14, 0%). The median total clinical scores for the ofloxacin (0.5) and moxifloxacin (0.8) groups were significantly (P=0.008, Mann-Whitney Test (MW)) lower than gentamicin (5.7), chloramphenicol (17.5), polymyxin B/trimethoprim (21.2), povidone-iodine (15.5), and saline (18.7). The FQs, ofloxacin and moxifloxacin, were more effective in preventing endophthalmitis than the non-FQ antibacterial agents in a rabbit S. aureus endophthalmitis model. The observed results are consistent with the hypothesis that FQs penetrate into the anterior chamber at more effective levels than many of the common non-FQ antibacterial agents.