Background: Budd-Chiari syndrome (BCS) is associated with parenchymal changes leading to major architecture remodelling. In order to gain further insight int o the pathogenesis of BCS, we investigated expression of a set of genes involved in the course of chronic liver diseases. Methods: Quantitative expression of 35 selected genes involved in extracellular matrix regulation, growth factors, and angiogenesis was investigated in 13 cases of BCS and compared with 10 normal li vers and 13 cirrhosis cases by real time reverse transcription-polymerase chain reaction. Differential gene expression was considered significant for genes sho wing at least a two-fold variation, with p< 0.05. Results: Expression of 14 gen es was significantly increased in BCS versus normal liver, with the highest incr ease in superior cervical ganglion 10 (SCG10) gene. BCS cases were classified ac cording to their evolution and morphological pattern as either acute or chronic in six and seven cases, respectively. Unsupervised hierarchical clustering of ac ute and chronic BCS cases on the basis of similarity in gene expression pattern led to distinction between the two groups. Expression of three genes was signifi cantly different in acute versus chronic BCS (increase in matrix metalloproteina se 7 and SCG10, decrease in thrombospondin-1 for chronic BCS). Seventeen and 10 genes, mainly involved in extracellular matrix and vascular remodelling, were s ignificantly deregulated in acute BCS versus normal liver and cirrhosis, respect ively. Conclusion: These results show that BCS cases display a specific gene exp ression profile that is different from that of normal liver and cirrhosis; the m olecular configuration of BCS can be readily distinguished by its evolution and morphological pattern. Background: Budd-Chiari syndrome (BCS) is associated with parenchymal changes leading to major architecture remodeling. In order to gain further insight into the pathogenesis of BCS, we investigated expression of a set of genes involved in the course of chronic liver diseases. Methods: Quantitative expression of 35 selected genes involved in extracellular matrix regulation, growth factors, and angiogenesis was investigated in 13 cases of BCS and compared with 10 normal li vers and 13 cirrhosis cases by real time reverse transcription-polymerase chain reaction. Differential gene expression was considered significant for genes sho wing at least a two-fold variation with p <0.05. Results: Expression of 14 gen es was significantly increased in BCS versus normal liver, with the highest incr ease in superior cervical ganglion 10 (SCG10) gene BCS cases were classified ac cording to their evolution and morphological pattern as either acute or chronic in six and seven cases, respectively. U nsupervised hierarchical clustering of ac ute and chronic BCS cases on the basis of similarity in gene expression pattern led to distinction between the two groups. Expression of three genes was signifi cantly different in acute versus chronic BCS (increase in matrix metalloprotein se 7 and SCG10, decrease in thrombospondin-1 for chronic BCS). Seventeen and 10 genes, mainly involved in extracellular matrix and vascular remodeling, were s ignificantly deregulated in acute BCS versus normal liver and cirrhosis, respect ively. Conclusion: These results show that BCS cases display a specific gene exp ression profile that is different from that from normal liver and cirrhosis; the m olecular configuration of BCS can be easy to be distinguished by its evolution and morphological pattern.