Carboxyfluorescein levels in ocular tissues of normal rats were measured using quantitative fluorescence microscopy and compared with fluorescein levels to determine the extent to which blood-retinal barrier permeability is affected by the difference in lipid solubility of these two dyes. Retinal fluorescence intensity measurements at 2 min after i.v. dye injection were very much lower for carboxyfluorescein than for fluorescein despite similar plasma free dye concentrations. Marked leakage of dye from the optic disc into peripapillary retina was identified. At 1- and 2 hr, retinal levels of the two dyes became more similar, because fluorescein was removed from retina faster than carboxyfluorescein. After sodium-iodate-induced damage of the pigment epithelium, high levels of both dyes were evident in retina, but carboxyfluorescein was localized chiefly within extracellular space whereas fluorescein also densely stained cell somata. The fluorescence intensity levels recorded, which are proportional to the total mass of dye in the tissue, were correspondingly lower for carboxyfluorescein than for fluorescein, indicating that they were markedly affected by the different distribution of the two dyes. To relate tissue fluorescence intensity directly to dye concentration in the extracellular fluid, measurements were obtained from isolated retinas incubated in dye solutions of known concentration. Log-log plots demonstrated a linear relation between fluorescence intensity and medium concentration for both dyes, but retinal fluorescence of carboxyfluorescein, in correspondence with its limited distribution in the tissue space, was consistently less than that of fluorescein. The ratio of carboxyfluorescein to fluorescein fluorescence varied with the retinal layers but was constant for each layer over the concentration range tested. These fluorescence intensity ratios then were used to adjust the in vivo data so that comparison between the two dyes more closely reflected their extracellular dye concentration. With this correction the amount of carboxyfluorescein present in outer retina shortly after dye injection was approx. 1/10 that of fluorescein, indicating that carboxyfluorescein penetrates the pigment epithelium less readily than fluorescein, as expected from the difference in lipid solubility of the two dyes. However, fluorescence of both dyes in retina and presumably in vitreous humor eventually reached similar levels. This is attributed to entry of the dyes at sites of barrier discontinuity, as at the optic disc, and by a difference in their rates of removal from the intraocular compartment.