Abstract Background Pancreatic sepsis can occur after contrast injection into an obstructed or disrupted pancreatic duct. Whether stents cause or prevent pancreatic sepsis is unknown. Accordingly, the pancreatic duct bacteriology in patients with pancreatic duct stents was retrospectively reviewed and contrasted with biliary cultures taken from patients at the time of bile duct stent retrieval and/or exchange. Methods Of 61 patients (29 men, 32 women; 72 stents; mean age 51  years, range 14–88 years), 36 with pancreatic duct stents had pancreatic duct cultures obtained at the time of stent exchange and/or retrieval. The results of these cultures were compared with bile duct cultures taken from 36 patients at the time of biliary stent exchange/retrieval. Eleven of the 36 patients with pancreatic duct stents also had bile duct stents. Data collected included stent patency, clinical sepsis at initial stent placement or retrieval, administration of antibiotics before the procedure, indication for stent placement, stent duration, and culture results. Results At stent retrieval and/or exchange, all 61 patients with pancreatic and/or biliary stents had contamination of the respective ducts with multiple enteric bacteria (mean 3.4 organisms in patients with pancreatic duct stents vs. 3.3 in those with bile duct stents). Clostridium perfringens was found in 17% and 0% of patients with, respectively, bile duct and pancreatic duct stents. Among the most common indications for pancreatic duct stent placement were stricture (28), sphincterotomy (9), leak (7), stones (3), and dilated pancreatic duct (1). Indications for a biliary stent included benign stricture (29), malignancy (6), stones (2), cholangitis (1), chronic pancreatitis (1), and dilated common bile duct (1). Pancreatic cultures were taken at a median of 85 days (interquartile range 60–126; range 13–273) and biliary cultures at a median of 87 days (interquartile range 45–149; range 19–927) after stent placement. Eleven patients, 6 with a bile duct stent, 4 with a pancreatic duct stent, and one with dual stents, developed pre-exchange/retrieval clinical sepsis; 3 had pancreatic sepsis. All had received antibiotics at initial placement. In the 11 patients with sepsis (12 stents), 8 stents were completely occluded at exchange/retrieval, 3 were partially occluded, and one was patent. In 50 patients (60 stents), no clinical sepsis developed; 7 stents were patent, 31 partially occluded, and 22 completely obstructed. Conclusions (1) Comparable to patients with biliary stents, all patients with pancreatic stents had contamination of the pancreatic ductal system by enteric flora. (2) In contrast to the 17% of patients with bile duct stents who had intraductal Clostridium perfringens, there were no instances ofcontamination with this organism in patients with pancreatic stent ( p = 0.025), although, after adjusting for multiple comparisons, statistical significance was lost. (3) There was a tendency for stent occlusion to predispose to pancreatic sepsis, but occlusion by itself was insufficient ( p = 0.106). (4) Further investigation is required to define the additional variables that are associated with the development of pancreatic sepsis.