Background: Bacterial community structures in human pancreatic and biliary tr acts were evaluated. Methods: Gall bladder stones from 153 patients, 20 gall bla dder walls, six common duct stones, 52 biliary stents, 21 duodenal biopsies, nin e pancreatic duct biopsies, and five bile ducts were investigated using fluoresc ence in situ hybridisation (FISH) with ribosomal RNA targeted Cy3/Cy5 (carbocyan ine) labelled oligonucleotide probes. Result: Duodenal, gall bladder, and bile d uct walls were free of bacteria. A dense multispecies bacterial biofilm was pres ent within the pancreatic duct of patients with calcific pancreatitis and within biliary stents, irrespective of diagnosis. The concentration, density, and amen ability of the biofilm to FISH and DNA staining declined progressively with the grade of stent occlusion. The lowest detectable bacterial concentrations were fo und by FISH in completely occluded stents and brown/mixed gall stones. Bacteria were not detectable with FISH in cholesterol gall stones. Conclusions: A wide ra nge of different branches and groups of bacteria participate in the development of biofilms on the surfaces of foreign bodies, such as biliary stents, mixed gal l stones, or calcific pancreatic ducts, but not on the surface of pure cholester ol gall stones. Occlusion of stents leads to progressive extinction of the biofi lm and mummification of its components. Deposition of cholesterol or other subst ances within the biofilm matrix may be a novel mechanism of host defence against bacteria present in these biofilms. Background: Bacterial community structures in human pancreatic and biliary tr acts were evaluated. Methods: Gall bladder stones from 153 patients, 20 gall bla dder walls, six common duct stones, 52 biliary stents, 21 duodenal biopsies, nin e pancreatic duct biopsies, and Five bile ducts were investigated using fluorescence in situ hybridisation (FISH) with ribosomal RNA targeted Cy3 / Cy5 (carbocyananate) labeled oligonucleotide probes. Results: Duodenal, gall bladder, and bile d uct walls were free of bacteria. A dense multispecies bacterial biofilm was pres ent within the pancreatic duct of patients with calcific pancreatitis and within biliary stents, irrespective of diagnosis. The concentration, density, and amen ability of the biofilm to FISH and DNA staining declined progressively with the grade of stent occlusion. The lowest detectable bacterial concentrations were fo und by FISH in completely occluded stents and brown / mixed gall stones. Bacteria were not detectable with FISH in c holes in gallium. Conclusions: A wide ra nge of different branches and groups of bacteria participate in the development of biofilms on the surfaces of foreign bodies, such as biliary stents, mixed gal l stones, or calcific pancreatic ducts, but not on the surface of pure cholester ol gall stones. Occlusion of stents leads to progressive extinction of the biofi lm and mummification of its components. Deposition of cholesterol or other subst ances within the biofilm matrix may be a novel mechanism of host defense against bacteria present in these biofilms.