The effects of two intraocular pressure (IOP)-lowering agents, latanoprost with 0.02% benzylalkonium chloride (BAK) and travoprost Z without BAK, on corneal epithelial permeability, assessed by carboxyfluorescein uptake, were compared in a rabbit cornea model (n = 12). Loss of epithelial tight junctions was measured by ruthenium red uptake with transmission electron microscopy. There was a significant difference between corneal epithelium permeability of rabbits exposed to either travoprost Z or latanoprost preserved with 0.02% BAK (P < 0.0001). There was no difference between untreated controls and those receiving travoprost Z (P = 0.224). Epithelial permeability was significantly increased in the corneas of rabbits exposed to latanoprost in the 3-min drop test (2.16 +/- 1.094 nm/sec) and the 3-min exposure (16.69 +/- 3.15 nm/sec), compared with control or travoprost (P = 0.002), likely due to the presence of a 0.02% concentration of BAK in the latanoprost solutions. There was no detectable loss of epithelial tight junctions in corneas from the control or travoprost Z groups, compared with significant loss in the latanoprost group. Agents such as travoprost Z with an alternative preservative decreased the epithelial toxicity associated with the long-term use of IOP-lowering agents preserved with BAK.