Patients with liver disease or systemic pathology are more prone to develop portal vein thrombosis. Non-neoplastic thrombosis is characterised by absence of intrathrombotic perfusion, corresponding to marked hypoechogenicity at contrast-enhanced ultrasound. We report two cases of portal vein thrombosis in which contrast-enhanced ultrasound showed marked hypoechogenicity in the late phase. This late phase perfusional contrast pattern is consistent with non-neoplastic thrombosis, but is actually similar to that of metastatic liver lesions. Echo-guided needle biopsy indeed yielded histological results consistent with carcinoma. Repeated contrast-enhanced ultrasound showed presence of intratumoural perfusion in the arterial phase, suggestive of the neoplastic nature of the thrombus. Our cases suggest that CEUS with second generation contrast agents in patients with portal thrombosis should include the evaluation of both arterial and portal phases in order to provide accurate non-invasive diagnosis of metastatic portal vein thrombosis.