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<b>AIM:</b> To compare the trabecular meshwork (TM) and iris apoptosis of treated and untreated primary open angle glaucoma (POAG) patients.<b>METHODS:</b> 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.<b>RESULTS:</b>The mean patient age was 60.6±5.8 years (53-68 years)<i> vs</i> 58.9±8.9 years (47-70 years) in group 1 and group 2 (<i>P</i>=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) (<i>P</i>=0.004, 0.015; respectively).<b>CONCLUSION:</b> Long term administration of topical antiglaucoma medications causes additional toxic effects on TM.