Purpose: The authors compared the effectiveness of limbus- and fornix-based conjunctival flaps in patients undergoing combined phacoemulsification, intraocular lens implantation, and mitomycin C trabeculectomy. Methods: The authors conducted a retrospective review of the records of 52 consecutive eyes of 45 patients who underwent combined surgery with limbus- and fornix-based conjunctival flaps, All surgery was by done by one surgeon on predominantly white patients in a suburban glaucoma subspecialty practice. Seven patients had both limbus- and fornix-based surgery, permitting fellow eye comparisons in these patients. All patients had at least 6 months and a median of 17 months follow-up. None of the eyes that were operated on had undergone intraocular surgery previously. Results: No clinically significant difference in postoperative pressure reduction, bleb survival, or visual acuity was seen between the fornix- and limbus-based groups. Results in the fellow eye comparison subgroups were similar. The mean intraocular pressure decreased from 20.4 mmHg before surgery to a mean of 12.4 mmHg at the last follow-up visit. Forty-seven (90.3%) of 52 eyes had a final best-corrected visual acuity of 20/40 or better. Forty eyes (76.9%) no longer needed antiglaucoma medications at the end of follow-up. Five eyes had intraoperative posterior capsule rupture; all of these occurred in the limbus-based group. Shallow serous choroidal effusions were more common in the fornix-based group, but none were clinically significant. No difference in postoperative astigmatism between the limbus- or fornix-based group was seen. Intraoperative pupilloplasty, synechialysis, or postoperative neodymium:YAG capsulotomy had no appreciable effect on final intraocular pressure or bleb survival. Endophthalmitis, aqueous misdirection, or hypotony maculopathy did not develop in any patient. Conclusion: The effectiveness of limbus- and fornix-based conjunctival flaps appears to be similar, The limbus-based technique may result in a higher incidence of posterior capsular rupture, but the safety of limbus- and fornix-based flaps is otherwise similar. Combined phacoemulsification and mitomycin C trabeculectomy appears to be safe and effective for treating selected patients with coexisting glaucoma and cataract.