To prospectively compare the influence of fornix-based and limbus-based conjunctival flaps on the final outcome and complications of 2-site phacotrabeculectomy with mitomycin-C in fellow eyes of patients with bilateral open-angle glaucoma (OAG). Glaucoma Unit, Department of Ophthalmology, University of Crete, Crete, Greece.Twenty-two patients with bilateral primary OAG and 8 patients with bilateral exfoliative glaucoma had 2-site phacotrabeculectomy in both eyes. Eyes were randomly assigned to the fornix-based flap or limbus-based flap group by the use of random tables. The intraocular pressure (IOP) decreased significantly in both groups (P <.01); however, there was no statistically significant difference between the groups in the amount of IOP decrease or the number of postoperative antiglaucoma medications after a 1-year follow-up. Faster improvement in visual acuity was observed in the fornix-based group during the first week. The mean time of surgery was 3.5 minutes less in the fornix-based group. An increased incidence of fibrin exudation, pupillary membrane formation, and capsule opacification was found in eyes with exfoliative glaucoma. The early bleb leakage was 3 times more frequent in the fornix-based group. The type of conjunctival flap in a 2-site phacotrabeculectomy did not seem to influence the final outcome. The main advantage of the fornix-based conjunctival flap is the shorter surgical time and the relatively faster improvement in vision postoperatively. The main disadvantage is more frequent early bleb leakage.