Surgical necrosectomy, but is still associated with a high morbidity. Indications of the endoscopic route, a new less invasive technique are not defined yet. To compare characteristics and clinical outcome of patients treated by the two techniques, a bi-centric retrospective comparison of 21 patients treated by surgical necrosectomy in one center (group S) with 11 patients treated in another center by endoscopic transgastric necrosectomy (group E) was performed. Clinical severity scores were significantly higher in group S although CT severity score did not differ between groups. Acute postoperative complications including pancreatic fistula occurred more frequently in group S (86% vs. 27%, P=0.002). ICU and hospital length of stay were higher in group S (84 vs. 4 days; P=0.008 and 58 vs. 15 days; P=0.005 respectively). Long-term complication did not differ between groups. Compared to surgery, endoscopic necrosectomy exhibited lower rate of complications and reduced hospital length of stays. Endoscopic transgastric necrosectomy appears as a safe and effective procedure and has to be included in the therapeutic algorithm of infected pancreatic necrosis.