A 42-year old man, 1 year previously diagnosed with ulcerative colitis after an emergency subtotal colectomy with formation of an ileostomy because of severe colitis with perforation, was admitted with sepsis and jaundice. The liver enzymes were elevated and blood cultures were positive for Streptococcus milleri. Magnetic resonance imaging showed a complete thrombosis of the main stem of the portal vein with occlusion of the left branch. Intravenous antibiotic therapy combined with heparinisation led to complete recanalisation of the thrombus. Portal vein thrombosis is a rare complication of inflammatory bowel disease and has been described in only 10 patients thus far. Multiple aetiologic factors may be responsible in relation to inflammatory bowel disease, such as hypercoagulability, thrombocytosis and abdominal sepsis. In patients with inflammatory bowel disease, unexplained sepsis and abnormal liver function tests, the possibility of an acute portal vein thrombosis should be considered and investigated, because unrecognised it may have serious long-term complications.