The reason why 10% to 20% of all patients with primary sclerosing cholangitis (PSC) develop cholangiocarcinoma (CC) remains unknown. The aim of this study was to compare the clinical and biochemical presentation in PSC patients with and without hepatobiliary malignancy and to look for risk factors for developing hepatobiliary carcinoma in PSC. All PSC patients (n = 20) with hepatobiliary carcinoma treated at Huddinge Hospital between 1984 and 1995 were age- and sex-matched to 20 PSC patients with end-stage disease without carcinoma. Clinical and biochemical data from four different occasions (time of onset of PSC, 12 and 6 months before and at the time of cancer diagnosis or liver transplantation [Ltx]) were registered. Seventeen patients had CC, 2 had hepatocellular carcinoma (HCC), and 1 had gallbladder carcinoma (GBC). Eighteen of the cancer patients and 19 controls had inflammatory bowel disease (IBD). The number of patients who smoked or were former smokers was significantly higher in the cancer group (P < .0004). The duration of IBD and PSC, extra- and intrahepatic distribution of PSC, surgical and medical treatments did not differ between the two groups. Abdominal pain was the only symptom that was more frequent among cancer patients at the time of cancer diagnosis/Ltx compared with controls. Evaluation of biochemical data did not indicate a more rapid deterioration among cancer patients. The mean value of the tumor marker, CA 19-9, in the cancer group was 700 kU/L; in the control group, it was 46 kU/L (P < .05), although data were only available in 10 cancer patients and 7 controls. Bile duct dysplasia was found in over 60% of patients with PSC and CC in nontumorous liver tissue apart from the tumor. Clinical and biochemical presentation of PSC patients with and without hepatobiliary carcinoma did not differ during the year before cancer diagnosis/Ltx. Smoking seems to be a risk factor for developing hepatobiliary carcinoma in patients with PSC.