The molecular basis to autoimmune arthritis is unclear. To identify candidate molecules that may be involved in the development and progression of collagen-induced arthritis (CIA), an animal model for human rheumatoid arthritis, we used microarray and real-time PCR assays to examine the gene expression profiles at the onset, peak and decline phase of CIA. Our results showed that, of the 514 immune-related genes assayed in microarrays, fifty-eight genes showed differential expression with thirty-one up-regulated and twenty-seven down-regulated in CIA joints, in comparison to normal joint tissue. By real-time PCR, expression of some chemokines/chemokine receptors, such as CCR1, CXCR4, CXCL13 and MCP1, showed significantly elevated in the inflamed joints. Quite a few genes were significantly up- or down-regulated at the peak time point, which indicates their roles in the progression of the disease. In addition, the expression levels of some genes remained significantly elevated at all stages of the disease. These gene expression profiles may help understand the pathogenesis of the disease.