Helicobacter pylori (H. pylori) DNA has been identified in human livers and has been implicated in chronic liver disease and liver cancer. To better understand the role of H pylori in primary sclerosing cholangitis (PSC), 25 patients with end-stage PSC and 31 controls were studied. Genomic DNA was extracted from microdissected hilar hepatic ducts of liver explants and was amplified for H pylori DNA. Serum was tested for H pylori antibodies. Helicobacter DNA was detected in 9 of the 56 (16%) patients by 16SrRNA PCR (an additional case [for a total of 18%] was antibody positive). Seven of the 9 cases identified by polymerase chain reaction were positive for the CagA gene, confirming they were H pylori. Seven of the 25 (28%) patients with PSC and 3 of the 31 (9.7%) controls were positive for Helicobacter (P=.087). H pylori DNA was detected in microdissected hilar biliary epithelium in more PSC patients than controls, supporting the hypothesis that bile reflux from the duodenum into the biliary tract might carry H pylori organisms into the proximal biliary system, possibly contributing to PSC development and/or progression in some patients.