Objective To investigate the diagnosis of organized thrombus in portal vein (PVOT) in liver transplantation. Methods The clinical data of 32 patients with PVOT who took the orthotopic liver transplantation (OLT) from January 2005 to January 2006 (271 cases) in this institute were retrospectively analyzed. Color doppler imaging (CDI), double helical CT plus three dimensional CT angiography (CTA) were taken before operation. CDI was performed during operation to look for the varicose vein, it was also used to reconstruct portal vein and measure the blood velocity in the portal vein. Results 23/32 (71.8%) cases had taken surgical treatment or interventional therapy before OLT. The grades of thrombus were as follows: gradeⅠ, 14/32; grade Ⅱ, 11/32; grade Ⅲ, 1/32; grade Ⅳ, 6/32. Twenty-eight cases of PVOT were diagnosed before operation, with accuracy of 87.5%. CDI was performed in 20 cases during operation, and 17 cases of collateral shunts were ligated with the monitor of ultrasound after the reconstruction of portal vein. The mean velocity of portal vein was (30.13±16.41) cm/s before the ligation of shunting veins, and the mean velocity was (46.36±19.82) cm/s after ligating the shunt veins. Conclusion Posibility of having PVOT for patients who had surgical treatment before OLT were much higher than who did not. CT and CTA could evaluate the portal vein system before operation, and performing CDI during operation may be important for the optimal reconstruction of portal vein.