Rheumatoid arthritis is a chronic autoimmune disease involving progressive destruction of the joints. Although a variety of antirheumatic drugs are in use, they usually only slow, and not halt, disease progression, or reverse the damage to cartilage and bone. Furthermore, treatment has to be discontinued in some cases due to toxicity and/or lack of response. By analyzing the whole transcriptome of a cell or tissue with microarray technology, a newo way of identifying treatments and discovering more about the mechanisms of known drugs has become available. This review discusses the strengths and weaknesses of microarray technology and gives an overview of gene expression studies currently performed in the field of antiheumatic therapies.