New experimental approaches of molecular medicine such as transcriptome and proteome analysis have been implemented in rheumatology research. Two-dimensional gel electrophoresis in combination with mass spectrometry was used to visualize and to identify proteins in synovial fluid (SF) and plasma samples from patients with rheumatoid arthritis (RA) and osteoarthritis (OA). The small calcium binding protein S100A9 (MRP14) was identified as a discriminatory marker protein in SF by global proteomic analysis. To confirm these results and to examine the reproducibility and the applicability as a diagnostic marker, levels of the S100A8 (MRP8)/A9 (MRP14) heterocomplex in plasma and in synovial fluid were validated from patients with RA, OA, and other inflammatory joint diseases using enzyme immunoassay techniques. It was found that plasma levels of the S100A8/A9 heterocomplex correlate well with levels in SF, and hence, determination of plasma levels can be used to distinguish RA patients from patients with other inflammatory joint diseases, as well as from OA patients and controls. Initial studies on RA patients also indicate that plasma levels of the S100A8/A9 heterocomplex are a useful marker in monitoring anti TNFalpha therapy.