Introduction: Knowledge of microbiology in the prognosis of patients with necrotizing pancreatitis is incomplete. Aim: This study compared outcomes based on primary and secondary infection after surgery for pancreatic necrosis. Method: From a limited prospective database of pancreatic necrosectomy, a retrospective case note review was performed ( October 1996 to April 2003). Results: 55 of 73 patients had infected pancreatic necrosis at the first necrosectomy. 25 of 47 patients had resistant bacteria to prophylactic antibiotics (n = 21) or did not receive prophylactic antibiotics ( n = 4), but this was not associated with a higher mortality ( 9 of 25) compared to those with sensitive organisms ( 4 of 22). Patients with fungal infection ( n = 6) had a higher initial median (95% CI) APACHE II score compared to those without (11 (9-13) verus 8.5 ( 7 - 10), p = 0.027). Five of six patients with fungal infection died compared to 13 of 47 who did not ( p = 0.014). With the inclusion of secondary infections 21 (32%) of 66 patients had fungal infection with 10 (48%) deaths compared to 11 (24%) of 45 patients without fungal infection ( p = 0.047). Conclusion: Whether associated with primary or secondary infected pancreatic necrosis, fungal but not bacterial infection was associated with a high mortality. Copyright (C) 2004 S. Karger AG, Basel.