Background: To determine the effect of scleral flap size on the medium-term intraocular pressure control and complication rates after augmented trabeculectomy. Design: Prospective randomized clinical trial. Participants: Glaucoma patients undergoing primary trabeculectomy. Exclusion criteria included previous ocular surgery apart from cataract surgery, secondary glaucoma and age under 18. Methods: Patients were randomized to either standard trabeculectomy (4 x 4 mm scleral flap) or microtrabeculectomy (2 x 2 mm scleral flap), both with adjustable sutures and antimetabolites. Bleb needling was performed as required. Patients were evaluated at day 1, weeks 1, 3, 6 and months 3, 6, 12, 18 and 24 postoperatively. Main Outcome Measures: Vision, intraocular pressure, complications and failure (intraocular pressure >= 21 mmHg or not reduced by >= 20% from baseline, intraocular pressure <= 5 mmHg, repeat glaucoma surgery and no light perception vision). Results: Forty-one patients were recruited; 20 had standard trabeculectomy, and 21 had microtrabeculectomy. At 2 years, the mean intraocular pressure and cumulative probability of failure was 12.4 +/- 4.6 mmHg and 0.28 for standard trabeculectomy, and 11.5 +/- 3.6 mmHg and 0.27 for microtrabeculectomy (P = 0.50 and 0.89, respectively). One patient in each group required Baerveldt device implantation. Vision reduced >= 2 Snellen lines in 15% in the standard trabeculectomy group and 25% in the microtrabeculectomy group, mainly from cataract (P = 0.48). Conclusion: Both trabeculectomy techniques achieved good intraocular pressure reduction and had similar complication rates. Scleral flap size had no significant effect on medium-term intraocular pressure control and complication profile.