Aims This study was designed to investigate the penetration of second-, third-and fourthgeneration topical fluoroquinolone into aqueous and vitreous humour in a rabbit endophthalmitis model. Methods Thirty New Zealand white rabbits were divided into six groups. Left eye was infected with an intravitreal inoculum of Staphylococcus aureus. Groups 1, 2, 3, 4, and 5 received topical ofloxacin, ciprofloxacin, lomefloxacin, levofloxacin, or moxifloxacin treatment 24 h after the inoculation, respectively. No treatment was given to group 6 as the control group (n ¼ 5). Aqueous and vitreous samples were obtained 30 min after the last drop. High-performance liquid chromatography was used to determine the fluoroquinolone concentration. Results In the normal and inflamed eyes, mean aqueous concentrations of ofloxacin were 1.90 and 2.69 lg/ml, ciprofloxacin were 2.16 and 3.65 lg/ml, lomefloxacin were 3.54 and 1.19 lg/ml, levofloxacin were 2.89 and 9.41 lg/ ml, and moxifloxacin were 4.92 and 43.33 lg/ ml, respectively. Mean vitreous concentrations of ofloxacin were 0.25 and 0.07 lg/ml, ciprofloxacin were 0.08 and 0.32 lg/ml, lomefloxacin were 0.001 and 0.03 lg/ml, levofloxacin were 0.03 and 0.09 lg/ml, and moxifloxacin were 0.28 and 2.68 lg/ml, in normal and inflamed eyes, respectively. Moxifloxacin achieved a significantly higher concentration in aqueous and vitreous humour of infected eyes compared with ofloxacin (Po0.01), ciprofloxacin (Po0.05), lomefloxacin (Po0.01), and levofloxacin (Po0.05). Conclusion This study demonstrated that fourth-generation fluoroquinolone, moxifloxacin, seems to have better penetration to inflamed ocular tissues in rabbit.