We compared complications between Ex-PRESS implantation and trabeculectomy for 2 years after surgery. Sixty-four open-angle glaucoma eyes were randomly assigned to treatment with trabeculectomy (n = 32) or Ex-PRESS implantation (n = 32). The primary outcomes were postoperative complications, including reduction of the endothelial cell density (ECD) of the cornea, cataract progression and the frequency of other late postoperative complications. The Ex-PRESS group had significantly greater reduction of postoperative corneal ECD than the trabeculectomy group did at 2 years after surgery (P = 0.026). Among the corneal areas measured using specular microscopy, the superior area, where the Ex-PRESS tube was inserted, had significantly more severe corneal ECD reduction than the inferior area after 2 years (-17.6% in superior area and -11.7% in inferior area, P = 0.04). More cataract progression occurred in the trabeculectomy group than in the Ex-PRESS group (P = 0.04). Twelve eyes (37.5%) in the trabeculectomy group and 4 eyes (12.5%) in the Ex-PRESS group underwent cataract surgery (P = 0.019). The total number of other postoperative complications between 3 months and 2 years was significantly higher in the trabeculectomy group than in the Ex-PRESS group (P = 0.02). Although Ex-PRESS implantation might be associated with an increased rate of corneal endothelial cell loss compared with trabeculectomy, it is beneficial for preventing cataract progression after filtering surgery.