Purpose To compare the effectiveness of limbus-and fornix-based conjunctival flaps in patients undergoing trabeculectomy with mitomycin-C augmentation. Methods A retrospective review of the records of 71 consecutive eyes of 59 patients who underwent trabeculectomy with mitomycin C. All the patients had at least 6 months of follow-up. The first 35 eyes underwent surgery with a limbal-based flap, whereas all subsequent surgeries were by fornix-based procedures. Results No significant difference was detected between the groups with regard to patient demographics, preoperative visual field and intraocular pressure parameters, postoperative intraocular pressures at day 1, months 1, 3, and 6 postoperatively, need for intervention, need for supplementary glaucoma medication, and final visual acuity. There were four cases of overdrainage and hypotony in the limbal-based group, whereas none occurred in the fornix-based group. In all 83% percent of eyes in the limbal-based group achieved intraocular pressures off medication of less than 18 mmHg, whereas 94% of the fornix based group obtained such IOP control. One patient in the limbal-based group developed late postoperative endophthalmitis. Conclusion Trabeculectomy with MMC augmentation is a safe and effective procedure for reduction of IOP and visual rehabilitation whether a fornix-or a limbal-based conjunctival flap is utilised. In this series, there was a greater risk of excessive drainage with subsequent hypotonous complications when surgery was undertaken by a limbal-based procedure.