Purpose: To compare the subjective symptoms, conjunctival hyperemia, tearing response and conjunctival cytological changes secondary to topical administration of bimatoprost and travoprost for 6 months. Methods: Newly diagnosed primary open-angle glaucoma patients were randomly prescribed bimatoprost (35 cases) or travoprost (42 cases). Two patients in each group were excluded because they did not appear at their appointments regularly. Thus, 33 and 40 patients completed the study in the bimatoprost and travoprost groups, respectively. Redness, itching, foreign-body sensation, pain and discomfort were assessed by a questionnaire, and patients were examined for conjunctival hyperemia. Schirmer’s I and break-up time tests were performed, and impression cytology of conjunctiva was evaluated. Results: Subjective symptoms were similar in both groups. The only subjective symptom that changed significantly was redness. The change in conjunctival hyperemia along the study period correlated with the patient-reported redness in both groups, being highest on day 30. Schirmer’s test I and break-up time did not change with time and were similar in both groups. The impression cytology grade increased with time in both groups with the only significant difference between groups on day 90 (higher in the bimatoprost group). Conclusion: We observed conjunctival hyperemia as the most common side effect of bimatoprost and travoprost. Tear film functions were not affected by these drugs while cytological alterations were.