Objectives Moxifloxacin (MXF), is a fluoroquinolone drug thought to have some antifungal activity against Candida albicans. The aim of our study was to investigate whether intravitreally and orally administered MXF has an effective penetration into the aqueous and vitreous in an experimental model of C.albicans endophthalmitis. Methods Thirty-two New Zealand rabbits were included. Endophthalmitis was induced in the right eyes of the rabbits. Left eyes were used as sham controls. Group 1 received a single dose of 160g MXF/0.1ml intravitreally. Group 2 received a single intravitreal dose of 160g MXF/0.1ml and an oral dose of 7mg/kg/day for 4 days. Group 3 received only an oral dose of MXF 7mg/kg/day for 4 days. Group 4 comprised of healthy controls. On the first and fourth day of treatment aqueous and vitreous samples were aspirated to compare the penetration of MXF. Key findings Between the first and fourth days, in group 1, mean MXF levels in the aqueous and vitreous tended to decrease; however, in group 3, these drug levels were tended to increase. There was also a decline in the drug levels in the aqueous and vitreous of group 2. Conclusions MXF cannot achieve sufficient penetration into the aqueous and vitreous of eyes infected with C.albicans.