Aqueous, corneal, and tear film 14C 5-fluorouracil (5-FU) levels were measured in rabbit eyes to better understand the mechanisms of intraocular penetration after subconjunctival injection. Significantly higher aqueous and tear 5-FU levels were achieved one hour after administration when the subconjunctival injection was given transconjunctivally rather than percutaneously through the upper lid [aqueous = 65.7 +/- 9.1 micrograms/ml vs 21.3 +/- 5.1 micrograms/ml (mean +/- SE; p = 0.02, 2-tailed t-test); and tears = 5408.8 +/- 357.3 micrograms/ml vs 228.0 +/- 46.4 micrograms/ml (mean +/- SE; p = 0.004, 2-tailed t-test)]. The aqueous 5-FU levels four hours after transconjunctival injection were significantly greater in anesthetized rabbits without blink reflexes than in those with intact reflexes [32.0 +/- 3.2 micrograms/ml vs 13.4 +/- 0.5 micrograms/ml (mean +/- SE; p = 0.026, 2-tailed t-test)]. The corneal 5-FU levels four hours after transconjunctival injection were greatest nearest the injection site. Direct corneal penetration appears to account for the majority of the aqueous 5-FU concentration after subconjunctival injection; however, there may also be diffusion through the limbus.