Abstract Background Biliary tract infection is a common cause of bacteraemia and is associated with high morbidity and mortality. Few papers describe blood culture isolates, underlying structural abnormalities and clinical outcomes in patients with bacteraemia. Aims To determine the proportion of bacteraemias caused by biliary tract infection and to describe patient demographics, underlying structural abnormalities and clinical outcomes in patients with bacteraemia. Design Prospective cohort study. Methods Biliary tract infection that caused bacteraemia was defined as a compatible clinical syndrome and a blood culture isolate consistent with ascending cholangitis. Patients aged 16 years and over were included in the study. From June 2003 to May 2005, demographic and clinical data were collected prospectively on all adult patients with bacteraemia. Radiological and endoscopic retrograde cholangiopancreatography findings were collected retrospectively. Results In 49 patients, the biliary tract was the site of infection for 39/592 (6.6%) community-acquired and 19/466 (4.1%) hospital-acquired episodes of bacteraemia. Three patients had mixed bacteraemias, and four had recurrent bacteraemia. The proportion of patients presenting with a structural abnormality was 34/49 (69%), and, of these structural abnormalities, 18/34 (53%) were pre-existing or newly diagnosed malignancies. Gram-negative organisms caused 55/58 (95%) episodes of bacteraemia. The most common Gram-negative organisms were Escherichia coli (34/55; 62%) and Klebsiella pneumoniae (14/55; 26%). Of the E coli isolates, 6/34 (18%) were extended spectrum β-lactamase producers or multiply drug resistant. Thirty-day mortality was 7/49 (14%). There was no difference in time taken to administer an effective antibiotic to survivors and non-survivors (0.86 vs 1.05 days, respectively, p = 0.92). Of the seven who died, four died from septic shock within 48 h of admission caused by “susceptible” Gram-negative organisms. Two others died from disseminated malignancy. Conclusions The proportion of bacteraemias caused by biliary tract infection was 5.5%. The most common infecting organisms were E coli and K pneumoniae. There was a strong association with choledocholithiasis and malignancies, both pre-existing and newly diagnosed. Death was uncommon but when it occurred was often caused by septic shock within 48 h of presentation.