To compare the success and complications of trabeculectomy performed with limbus-based and fornix-based conjunctival approaches. Retrospective case series with some prospective data collection. Consecutive patients undergoing trabeculectomy by 2 surgeons between May 2000 and October 2008. We performed limbus-based operations during the first 4 years and fornix-based operations during the last 4 years. We collected data by chart review and by examination at the most recent visit. For each follow-up visit, we defined success as undergoing no further glaucoma procedure and achieving one of our intraocular pressure (IOP) criteria. We used Kaplan-Meier survival analysis, Cox proportional hazards models, and generalized estimating equation (GEE) analysis. During 2009, 439 trabeculectomy sites of 347 patients were quantitatively assessed by the Indiana bleb grading system. (1) Success rate of trabeculectomy, as determined by the achievement of each of our different IOP goals, with or without IOP-lowering medications; and (2) incidence of surgical complications. During the 4 years after surgery, the success rates of limbus-based and fornix-based trabeculectomy were not statistically different for any of our IOP criteria. Blebs after limbus-based surgery were more likely to be graded as higher and to be avascular (GEE model, both P < 0.0001). Four percent of eyes experienced late-onset bleb leaks within 4 years after both limbus- and fornix-based operations; however, limbus-based cases developed bleb leaks significantly later than did fornix-based cases (2.1 vs. 1.0 years; P=0.002, GEE model). Late bleb-associated infection during the first 4 years after surgery occurred more often in limbus-based operations, although statistical significance was borderline (P=0.054, Cox model). Symptomatic hypotony during all available follow-up was more common with fornix-based operations (P=0.01, GEE model). Eyes undergoing the fornix-based operation had a greater risk of cataract surgery in the 4-year period after surgery (P=0.02, Cox model), and fornix-based cases requiring cataract surgery had the operation earlier than limbus-based cases (P=0.002, GEE model). Success rates are similar between limbus-based and fornix-based trabeculectomy. Limbus-based procedures produce higher, more avascular blebs, with a greater risk of infection. Fornix-based procedures have more symptomatic hypotony and more and earlier cataract development.