The ocular distribution of micafungin (MCFG), which has antifungal activity against Candida and Aspergillus species, was followed after the systemic administration of MCFG in rabbits. After MCFG (10 mg/kg) plus fluconazole (FLCZ; 10 mg/kg) was administered intravenously, the rabbits were killed, and MCFG and FLCZ concentrations in retina-choroid, vitreous humor, and plasma were determined by high performance liquid chromatography or liquid chromatography/mass spectrometry. The mean concentrations of MCFG in the retina-choroid at 0.25, 0.75, 4, 8, and 24 h after administration were 20.18, 15.97, 13.19, 6.27, and 0.75 microg/g, respectively, and were comparable with the MCFG plasma concentrations. The MCFG concentrations in retina-choroid and plasma exceeded the minimal antifungal inhibitory concentrations for endophthalmitis, although MCFG was not detected in the vitreous humor. These results suggest that the intravenous administration of MCFG is an effective treatment for endogenous fungal endophthalmitis when the causative fungus is localized in the retina and choroid.