Patients who develop veno-occlusive disease (VOD) of the liver may have low plasma levels of the natural anticoagulants protein C and antithrombin III, but large vessel thromboses are not commonly reported in these patients. We reviewed the records of 1847 consecutive patients for evidence of portal vein thrombosis. Eight patients (0.4%) developed portal vein thrombosis (PVT) at a median of day +28 (range 3-58). All patients had clinical evidence of VOD with ascites, a median total serum bilirubin 11.9 mg/dl, and median weight gain from baseline of 7.9%. Median plasma levels of antithrombin III and protein C were low (36% and 21%, respectively). Four patients with PVT died of severe VOD and multi-organ failure, but PVT did not contribute to death. We conclude that PVT is a rare complication of hematopoietic cell transplant and is associated with hepatic VOD. We speculate that PVT resulted from diminished portal venous flow (related to hepatic sinusoidal obstruction to blood flow) and a hypercoagulable state (related to low circulating antithrombin III and protein C levels). Prognosis depended on the severity of the underlying VOD and not PVT per se, suggesting that treatments directed solely toward dissolution of portal vein thrombi should be used with caution in this setting.