The characteristics and advantages of traditional Chinese medicine ( TCM ) diagnosis and treatment of chronic liver diseases are conducted on the individualized treatment based on TCM syndrome classification . In this study , the analysis of systems biology was carried out for TCM syndrome classification in chronic hepatitis B and posthepatitic cirrhosis . The relationship between TCM syndrome classification and genetic polymorphism , the difference of genes and protein expression profiles , the difference of urine metabolite , and the molecular mechanism of Different TCM Syndrome for Same Disease and Same TCM Syndrome for Different Diseaseswere discussed . The results showed that there are molecular biological basis in TCM syndrome classification in hepatitis B and posthepatitic cirrhosis . The systems biology based syndrome identification methods may be bene-ficial to form a new classification , and provide reference for the diagnosis and individual therapy of hepatitis B and posthepatitic cirrhosis .