AIM: To investigate the effect of long-term use of topically administered latanoprost on conjunctival thickness (CT) and conjunctival epithelium thickness (CET) in the patients with glaucoma. METHODS: A series of 106 glaucomatous patients were included. Of the 106 eyes, 55 eyes were treated with latanoprost eye drops once a day (latanoprost group), while 51 eyes were treated with carteolol hydrochloride eye drops (carteolol group). All the included patients completed a 2-year follow-up. CT and CET were measured with optical coherence tomography (OCT) in all patients at presentation and at 2-year visit, respectively. Statistical analysis was then performed to compare the change in CT and CET. RESULTS: At presentation, there was no difference in CET (t=0.400, P=0.689) or CT (t=1.14, P=0.259) between the two groups. No significant difference was found in CET (61.65±5.35 μm at baseline, 60.36±6.36 μm at 2-year follow-up, respectively; t=1.977, P=0.0531), while there was a significant decrease in CT from 201.45±14.99 μm at baseline to 167.81±14.57 μm at 2-year visit (t=14.1407, P<0.001) in the latanoprost group. At 2-year follow-up, no statistically difference was found in CET (62.24±5.27 μm; t=1.086, P=0.282) or CT (201.23±12.45 μm; t=1.44, P=0.154) compared to it at baseline (CET: 61.23±5.42 μm; CT: 198.76±13.68 μm, respectively) in the carteolol group. CONCLUSION: A significant decrease in conjunctival thickness is found in glaucoma patients treated with long-term topical latanoprost; its potential effect on the outcome of filtration surgery should be considered.