Epidemiological reports on risk and prognostic factors in patients with mesenteric venous thrombosis (MVT) are scarce. Patients with MVT were identified through the inpatient and autopsy registry between 2000 and 2006 at Malmö University Hospital. Fifty-one patients had MVT, diagnosed at autopsy in six. The highest incidence (11·3 per 100 000 person-years) was in the age category 70–79 years. Activated protein C resistance was present in 13 of 29 patients tested. D-dimer at admission was raised in all five patients tested. Multidetector row computed tomography (CT) in the portal venous phase was diagnostic in all 20 patients investigated, of whom 19 were managed conservatively. The median length of resected bowel in 12 patients who had surgery was 0·6 (range 0·1–2·2) m. The overall 30-day mortality rate was 20 per cent; intestinal infarction (P = 0·046), treatment on a non-surgical ward (P = 0·001) and CT not done (P = 0·022) were associated with increased mortality. Cancer was independently associated with long-term mortality: hazard ratio 4·03, 95 per cent confidence interval 1·03 to 15·85; P = 0·046. Portal venous phase CT appeared sensitive in diagnosing MVT. As activated protein C resistance was a strong risk factor, lifelong anticoagulation should be considered.