Evaluation of differentially regulated genes is essential for the development of novel therapeutic approaches in multifactorial diseases such as rheumatoid arthritis (RA). The analysis of the pathophysiology of RA requires also a functional understanding of the interactions between different cell types, the cell matrix, intracellular signaling pathways, often also called functional genomics, as well as between the different tissues in the joint such as cartilage, bone, adipose tissue, and the synovium. In addition, the identification of disease- or treatment-specific genes has become an important tool in arthritis research to determine novel molecular markers for diagnosis and monitoring of RA, and to elucidate the exact mode of operation and the potential target molecules for therapeutic intervention. Current approaches to analyze gene expression in arthritis are based on RNA isolated from cultured synovial cells or from synovial tissues and biopsies. Other approaches are directed to cultured cells such as RA synovial fibroblasts, one of the key players in inflammation and cartilage destruction, chondrocytes, macrophages or lymphocytes to characterize molecular changes and pathomechanisms in the RA synovium, especially at sites of adhesion and invasion of the synovium into the adjacent cartilage and bone. In this review, different methods to analyze gene expression of cells and tissues from patients with arthritides ranging from RNA fingerprinting to cDNA array are presented and discussed. In addition, a special focus is addressing the pitfalls resulting in over- or misinterpretation of the data obtained by these sensitive techniques.