A prospective and randomized clinical trial was conducted to investigate the pressure-lowering effect of mitomycin C-aided trabeculectomy in the Turkish population. The scleral tissues excised during the operation were examined by light and electron microscopy. The study population consisted of 26 patients undergoing mitomycin C-aided trabeculectomy and another 26 patients subjected to trabeculectomy without mitomycin C serving as controls. The treatment groups consisted of primary open-angle and closed-angle glaucomas, congenital glaucomas, various types of secondary glaucomas and prior failed trabeculectomies. The decrease in IOP was more marked (P < 0.01) and the number of additional medications needed post-operatively was less in the mitomycin C group (P < 0.01). There were no serious complications except for transient hypotony in one mitomycin-treated eye. Transmission electron microscopic examinations showed differences between the control and mitomycin applied trabecular blocks. At the scleral dissection plane where mitomycin was applied, collagen fibrils were frayed with a loss of proteoglycan cross-links. Fibroblasts demonstrated pyknotic nuclei and loss of cell processes. In the control group, active fibroblasts and regular collagen structure were observed at this level. The middle and inner scleral layers were generally unaffected except for minor changes in some of the mitomycin-treated eyes. Our study showed mitomycin C to be safe and effective as adjunct to trabeculectomy in both primary open-angle, primary angle-closure, various secondary glaucomas and prior failed trabeculectomies. Transmission electron microscopic examinations of excised blocks showed disruption in collagen organization and cytopathic effects to fibroblasts. Mitomycin seemed to affect the proteoglycan cross-links between collagen fibrils after its application.