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PURPOSE To compare the late complications in the Ahmed Baerveldt Comparison Study during 5 years of follow-up. DESIGN Multicenter, prospective, randomized clinical trial. METHODS SETTINGS Sixteen international clinical centers. STUDY POPULATION Two hundred seventy six subjects aged 18 to 85 years with previous intraocular surgery or refractory glaucoma with intraocular pressure of > 18 mmHg. INTERVENTIONS Ahmed Glaucoma Valve FP7 or Baerveldt Glaucoma Implant BG 101-350. MAIN OUTCOME MEASURES Late postoperative complications (beyond 3 months), reoperations for complications, and decreased vision from complications. RESULTS Late complications developed in 56 subjects (46.8 ± 4.8 5 year cumulative % ± SE) in the Ahmed Glaucoma Valve group and 67 (56.3 ± 4.7 5 year cumulative % ± SE) in the Baerveldt Glaucoma Implant group (P = 0.082). The cumulative rates of serious complications were 15.9% and 24.7% in the Ahmed Glaucoma Valve and Baerveldt Glaucoma Implant groups respectively (P = 0.034) although this was largely driven by subjects who had tube occlusions in the two groups (0.8% in the Ahmed Glaucoma Valve group and 5.7% in the Baerveldt Glaucoma Implant group, P = 0.037). Both groups had a relatively high incidence of persistent diplopia (12%) and corneal edema (20%), although half of the corneal edema cases were likely due to pre-existing causes other than the aqueous shunt. The incidence of tube erosion was 1% and 3% in the Ahmed Glaucoma Valve and Baerveldt Glaucoma Implant groups, respectively (P = 0.04). CONCLUSIONS Long term rates of vision threatening complications and complications resulting in reoperation were higher in the Baerveldt Glaucoma Implant than the Ahmed Glaucoma Valve group over 5 years of follow-up.