Objectives: To compare ocular surface changes induced via glaucoma treatment in patients using fixed combinations of bimatoprost 0.03%/timolol 0.50%, timolol 0.50% or bimatoprost 0.01% eye drops. Methods: This is a prospective, one center, open-label clinical trial. It was performed on 60 glaucoma patients between 01-01-2012 and 12-31-2012. These patients were randomly divided in three subgroups: bimatoprost 0.03%/timolol 0.50% fixed combination, timolol 0.50% and bimatoprost 0.01%. The Ocular Surface Disease Index (O.S.D.I.) was evaluated in all the glaucomatous patients of the three subgroups at basal time and after 6 and 12 months. All the results were statistically evaluated by Student t-test and one-way ANOVA. The results were considered statistically significant if p < 0.05. Results: All of the patients ended the clinical trial. There was no statistical significant difference between patients treated with the bimatoprost 0.03%/timolol 0.50% fixed combination and timolol 0.50% eye drops alone (p = 0.845). Instead, there was a statistically significant difference between bimatoprost 0.01% and bimatoprost 0.03%/timolol 0.50% patients (p = 0.05) and between bimatoprost 0.01% and timolol 0.50% eye drops alone (p = 0.049). Conclusions: This is a clinical trial based not on the hypotonising effect of these drugs but on their tolerability. The drug which showed the best tolerability is bimatoprost 0.01%.