OBJECTIVE: This study investigated the possible molecular mechanisms of pure total flavonoids from citrus (PTFC) for the treatment of non-alcoholic fatty liver disease (NAFLD) via toll-like receptor/C-C chemokine ligand (TLR/CCL) signaling pathways by monitoring the changes in gene expression profile in liver tissues induced by high-fat diet. METHODS: We performed systematical analyses on hepatic expression profiles of mRNAs in a high-fat diet (HFD)-induced steatotic animal model with or without PTFC treatment. The study was conducted by using MouseOneArray(?) v2 gene chip, and analyzed by bioinformatics tools for differential gene expression. Real time-PCR, Western blot and liquid suspension array analysis were used to validate specific genes in the NAFLD liver expression profile in which PTFC plays a role in the TLR/CCR pathway. RESULTS: We found that a total of 562 genes showed varying degrees of reversal after PTFC intervention. Pathway analysis of the differential gene expression in the HFD group and the normal diet group (ND group) revealed six signaling pathways related to inflammatory responses in the top ten results. Comparison of genes between the HFD+PTFC and the HFD groups indicated seven signaling pathways correlated with inflammatory response in the top ten results of the pathway analysis. The TLR/CCL inflammatory signaling pathways played an essential role during liver inflammation in NAFLD mice induced by high-fat diet. Real-time PCR, Western blot and liquid suspension array analysis of the differential gene expression involving the TLR/CCL signaling pathways validated the results of microarray detection. CONCLUSION: PTFC may improve NAFLD by regulating TLR/CCL signaling pathways. Genomic studies provide additional evidence supporting the role of PTFC in the treatment of NAFLD.