The aim of this study was to evaluate intraocular biodistribution of a fluorescent polymeric nanosystem composed of chitosan and gelatin after intravitreal administration in rat eyes. The nanoparticles based on chitosan and gelatin were synthesized using a reverse emulsion-double cross-linking technique (ionic and covalent) and their structural characteristics are presented. Two units of 1% suspension of fluorescein-labeled nanoparticles in saline solution were injected intravitreal in rat eyes. The histological cross-sections obtained at 24 and 72 hours were analyzed by confocal microscopy and compared to a similar number of control cross-sections. The scanning electron microscopy of the nanoparticles obtained by double cross-linking in reverse emulsion technique revealed spherical, smooth, highly porous particles with no tendency to form aggregates. The chitosan-fluorescein conjugate was present in all the ocular tissues both at 24 and at 72 hours. The nanoparticles were present in the retina in a larger quantity and persisted longer than in the other ocular tissues. They were mainly fixed paravascular. The double cross-linking in reverse emulsion technique was efficient in synthesizing a biocompatible polymeric nanosystem. The in vivo study of intraocular biodistribution of fluorescein-labeled nanoparticles revealed their affinity for the retina after intravitreal administration.