In Budd-Chiari syndrome (BCS), with reduced portal and venous outflow and hyperarterialization, regenerative nodules may develop during the course of the disease from hepatic atrophy and progressive fibrosis. Using contrast-enhanced CT, we aimed to determine the imaging characteristics of regenerative hepatic nodules, their incidence rates in both diagnosis and follow-up, and the yields of the CT scan technique confirmed by pathological examination and to evaluate the frequency and detection rate of hepatocellular carcinoma. This two-centered retrospective study included 33 patients with primary chronic BCS who received liver transplants. Before and after the contrast application, multiphase protocol was used for image acquisition during arterial, portal-venous, and delayed phases. CT angiography and three-dimensional tomography images were obtained. Primary outcome was the harmony between CT imaging findings and pathological results. Secondary outcome was relationship between nodule incidence rate in BCS and malignancy development rate in nodules, and relationship between nodule and HCC development and disease duration and blood type. In determining the pathologically diagnosed nodules, computed tomography had a sensitivity of 78.3%, positive predictive value of 90.0%, specificity of 80.0%, and negative predictive value of 61.5%. The incidence rate of HCC in all BCS cases was 9.1%, while the incidence rate was 13% among patients with regenerative nodules only. However, none of the patients with regenerative nodules and HCC had hepatitis. In all patients which had regenerative nodules and HCC, BCS was caused by hepatic venous obstruction, and HCC had developed in less than 5 years. Regenerative nodules developed in most patients with chronic primary BCS, and some of them had HCC. To our best knowledge, this is the first study to use the high yield rates in CT images to evaluate and monitor nodules that developed in the liver of the patients with primary BCS who were planned to undergo liver transplantation. Unlike previous studies that recommended HCC diagnosis and follow-up based solely on AFP and image characteristics, the present study recommends histopathological confirmation for suspicious nodules.