Our aim was to evaluate the effects of topical antiglaucomatous medications on conjunctival thickness using anterior segment optical coherence tomography (AS-OCT). Thirty eyes of 30 patients with primary open angle glaucoma, who had never used any antiglaucomatous medications, enrolled in this prospective study. Followed by a full ophthalmologic examination, the conjunctival thickness was measured before treatment and at 1, 3, and 6-month post-treatment by AS-OCT. Measurements were taken from the superior bulbar conjunctiva, 3-4 mm from the limbus. The mean age of patients was 67.7 ± 8.6; fourteen cases (46.7%) were given latanoprost, 2 cases (6.7%) brinzolamide+timolol, 2 cases (6.7%) betaxolol, 4 cases (13.3%) travoprost, and 8 cases (26.7%) brimonidine. The mean baseline conjunctival thickness was 222.9 ± 38 μm, while the mean conjunctival thickness was 212.8 ± 36.0 μm in the first month, 198.2 ± 35.8 μm in the third month, and 187.5 ± 40.2 μm in the sixth month. Decrease in conjunctival thickness at each examination was statistically significantly compared to baseline. (P < 0.05) Decrease in conjunctival thickness in Latanoprost subgroup was statistically significant, whereas the decreases in other active ingredients were not. Topical antiglaucomatous medications especially prostaglandin analogs may affect conjunctival thickness even during the first few months. This thinning effect may be crucial for the conjunctiva, as the basis of the possible filtration surgery.