Objective To explore the relationship between fatty liver TCM syndromes and gene polymorphism of PPAR-γ C161T and CYP Ⅱ E1. Methods 183 patients are differentiate by Chinese traditional medicine， BMI， WC， BP， FINS， FBG， HOMA -IR， liver and kidney function， serum lipid. PPARγC161-T， CYP Ⅱ E1 gene polymorphism and allele frequencies are detected in 183 cases of patients and 40 healthy persons. Results TG， TC， LDL-C of silt syndrome group and phlegm stasis syndrome group were higher than those without a discernible group（P<0. 05）. Compared with the control group， genotype and allele frequencies of PPAR-γC161-T of each fatty liver syndrome groups have no significant difference（P>0. 05）， while genotype and allele frequencies of CYP Ⅱ E1 of each fatty liver syndrome group have significantly difference（P<0. 05）. Conclusion Disorder of lipid metabolism and associated changes closely relate to silt and phlegm stasis syndrome. Gene polymorphism CYP Ⅱ E1 may play an important role in the formation and transformation of silt and phlegm stasis syndrome in fatty liver disease.