Three patients developed abdominal pain and abnormal liver enzymes without hyperbilirubinemia, early after autografting for lymphoma. Two had received conditioning therapy with busulfan, cyclophosphamide and continuous infusion etoposide; the other had received busulfan and melphalan. Doppler ultrasound in all cases demonstrated thrombosis of the main portal vein and its branches. In the two patients tested, transient deficiencies in protein C (both cases) and protein S (one case) were observed. One case was chronologically related to anti-fibrinolytic therapy and resolved spontaneously. The other two cases resolved after treatment with low molecular weight heparin. Portal vein thrombosis should be considered in the differential diagnosis of abdominal pain and liver dysfunction after BMT.