We studied prospectively the results of limbus-versus fornix-based flaps in patients undergoing combined trabeculectomy and phacoemulsification. We found no significant difference at six months postoperatively in the level of intraocular pressure between the limbus-(16.1 +/- 4.1 mm Hg) and fornix- (14.0 +/- 3.4 mm Hg, p = 0.161) based groups, or in the number of glaucoma medications (p = 0.0750). The highest intraocular pressure recorded within the first postoperative month was similar between groups (18.4 +/- 6.9 mm Hg for limbus and 18.5 +/- 5.5 mm Hg for fornix, p > 0.900). Postoperative bleb height, extent, and vascularity, as well as chamber depth were statistically similar between groups (p > 0.05). Postoperative complications were similar between groups. This study indicates that both fornix- and limbus-based flaps may be used safely and effectively when performing a trabeculectomy combined with phacoemulsification.