Background Bleb-associated endophthalmitis (BAE) is a rare but severe complication of trabeculectomy with poor outcome. Various surgical methods were explored to treat such patients. However, there is no defined protocol. The aim of this study was to describe a new combined operation, and to demonstrate the outcome of the treatment. Methods Nine patients with BAE were enrolled in our study. The combined operation including pars plana vitrectomy (PPV), sclera patch graft (SPG) and endoscopic cyclophotocoagulation (ECP) was used to treat these patients. Results In the follow-up of 18-24 months, all patients with the endophthalmitis were cured, the useful visual acuity was preserved in 7 patients, and the intraocular pressure (IOP) of 8 patients was controlled just after first operation, only one needed another trans-scleral cyclophotocoagulation. Conclusion This combined operation is a useful method for treating the patients with BAE, with SPG and vitrectomy to control the endophthalmitis and ECP to balance the postoperative IOP. Chin Med J 2012;125(18):3344-3345