Objective: To study the effects of Wenhua Juanbi recipe (WJR) on the gene expression profile of the synovium in collagen-induced arthritis (CIA) rats, and to explore its mechanisms for treating CIA., Methods: The CIA model was induced by intradermal injection of bovine collagen type II emulsion from the tail of 40 healthy male Wistar rats. Selected 16 successfully modeled rats were randomly divided into the model group and the WJR-treated group, 8 in each group. WJR at the daily dose of 22.9 g/kg was given to rats in the WJR-treated group by gastrogavage, while normal saline was given to those in the model group. Both were performed once daily, for 30 successive days. By the end of medication, the total RNA was extracted from the synovium of rats in the two groups. The gene expression profile of each sample was analyzed using Illumina oligonucleotide microarray., Results: Compared with the model group, after the intervention of WJR, 222 differentially expressed genes were identified in CIA rats, including 76 genes up-regulated (such as RatNP-3b and so on) and 146 downregulated (such as Angptl 2, Muc1, bcl-2, and so on). The differential genes were mainly involved with apoptosis, angiopoietin, defensin gene, cytokine, signal transduction, oncogene, etc., Conclusion: WJR played a role in treating CIA multi-target possibly through regulating and controlling multiple genes expressions. Wenhua Juanbi Recipe; collagen-induced arthritis; synovium; gene expression