Arthroscopy allows biopsy under direct visualization of synovial tissue from a knee joint early in the course of arthritis. Synovial tissue from patients with Rheumatoid Arthritis (RA) early in disease (< 12 months), late RA (>3 years) and Osteoarthritis (OA) were examined using the complementary techniques of in situ hybridization (ISH), monoclonal antibody based immunohistochemical analysis, and a novel form of Quantitative-Competitive Reverse Transcribed Polymerase Chain Reaction (QC-RT-PCR). The frequency of multiple cellular constituents including T cell subsets, B cells, and macrophages were determined using standard avidin-biotin-complex immunoperoxidase staining. Expression of genes for several inflammatory cytokines and metalloproteinases was assessed by ISH and QC-RT-PCR. These studies demonstrate abundant quantities of cytokines produced by macrophages and stromal cells such as TNFa, IL-lβ, and IL-6, but a paucity of T cell derived cytokines including IL-2, IFN-y, IL-4, and IL-10. Comparison between quantitative morphometric analysis of the ISH results and the QC-RT-PCR analysis on bulk tissue demonstrated concordance for individual cytokines within a single specimen. In some cases the extremely low amount of mRNA detected by QC-RT-PCR suggested less that one cell per section. The frequency of T cells within the synovial lining, which expresses abundant collagenase and stromelysin, was associated with early disease. These T cells were predominately CD8+ and IL-2R+. Supported by HL50724, and Sankyo Ltd.