We studied 20 patients with uncontrolled symmetric glaucoma who had undergone bilateral trabeculectomy after having received the same medical or laser treatment to both eyes. In each patient, the techniques and suture material used in the two eyes were identical, and the surgeon was the same. The only variable was the type of conjunctival flap used: one eye received a limbal-based flap and the other a fornix-based flap. These patients were followed up from three to 13 months (median, 8.5 months). There was no difference between the two groups in postoperative anterior chamber depth, intraocular pressure control, occurrence of hyphema, size and shape of the bleb, or the rate of complications. The fornix- and limbal-based conjunctival flaps in trabeculectomy were found to yield comparable results in terms of safety and short-term efficacy of pressure control.