Purpose.We evaluated ocular penetration and drug levels in tears after topical ofloxacin instillation in rabbit eyes with amniotic membrane transplantation (AMT).Methods.Forty-eight New Zealand White rabbits were used. In the first set of experiments, 24 rabbits (24 eyes) were divided into four groups according to the epithelial removal or AMT. Topical ofloxacin was instilled four times every 15 minutes. One hour after the last eyedrop, the concentration of ofloxacin in the amniotic membrane, cornea, and aqueous humor was evaluated. In the second set of experiments, 24 rabbits were divided into six groups according to AMT (transplantation of lyophilized or fresh amniotic membrane) or duration of application. Ofloxacin ointment or two drops of ofloxacin were applied to the right eye, and then tear samples were collected after 0.5, 1, 2, 4, and 6 hours for the analysis of ofloxacin concentration.Results.Mean ofloxacin concentrations in the cornea and aqueous humor were statistically higher in deepithelialized cornea regardless of AMT (p< 0.05). The mean tear levels of ofloxacin in the AMT groups were statistically higher than those in non-AMT groups (p< 0.05). There was no statistical significance in the tear level of ofloxacin between lyophilized amniotic membrane groups and fresh amniotic membrane groups nor between 1-hour amniotic membrane–attached groups and 6-hour amniotic membrane–attached groups.Conclusion.Amniotic membrane transplantation seems to interfere with the ocular penetration of topical ofloxacin in normal rabbit corneas but enhances ofloxacin penetration in corneas with epithelial defects. The ofloxacin level in tears was higher in eyes with AMT up to 1 hour after topical ofloxacin use. Therefore, it seems that amniotic membrane has some potential to act as an effective drug delivery system.