AIM: To compare the trabecular meshwork (TM) and iris apoptosis of treated and untreated primary open angle glaucoma (POAG) patients.METHODS: Eight treatment-naive, newly diagnosed (group 1) and 11 medicaly treated (group 2) patients with POAG were included in the study. Each patient underwent a limbus-based trabeculectomy. The TM and peripheral iris specimens were dissected out and were snap-frozen in liquid nitrogen and stored at –80℃ until they were assayed. Apoptosis in each group was assesed by TUNEL method.RESULTS:The mean patient age was 60.6±5.8 years (53-68 years) vs 58.9±8.9 years (47-70 years) in group 1 and group 2 (P=0.859). The mean treatment time in group 2 was 22.2±7.3 months (12-34 months). Apoptotic indexes in TM and iris were significantly higher in POAG patients using medication (group 2) compared to treatment-naive POAG patients (group 1) (P=0.004, 0.015; respectively).CONCLUSION: Long term administration of topical antiglaucoma medications causes additional toxic effects on TM.