Background: To investigate the effects of topical antiglaucoma drugs on apoptosis rates of conjunctival epithelial cells in vivo. Methods: Specimens were obtained from the bulbar conjunctiva of 30 patients who underwent either cataract or glaucoma surgery. Of these 30 patients, 14 had glaucoma and received topical antiglaucoma drugs. The 16 patients in the control group had neither systemic nor ocular disease except cataract and they did not receive any medications. TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick-end labelling) method was used to show the apoptosis of the conjunctival epithelial cells. Results: Increased apoptosis rates were detected in specimens of patients who were on topical antiglaucoma therapy (mean ± SD 0.208 ± 0.154) when compared with the healthy subjects (mean ± SD 0.083 ± 0.102; P = 0.013). The apoptosis rates did not differ according to type, number or duration of drugs. Conclusions: The apoptosis observed in the conjunctival epithelial cells might be due to the preservative benzalkonium chloride in the antiglaucoma medications because the apoptosis rates did not differ in patients using different types of medications.