OBJECTIVES: To determine whether type IX collagen-related peptides can be detected in the synovial fluids of arthritis patients and to assess their potential as molecular markers of arthritis. PATIENTS/METHODS: Synovial fluids from a set of carefully diagnosed arthritis patients and from healthy volunteers were used. Hydroxyproline assays were carried out to determine the content and concentration of collagen. Collagen cross-link determinations were conducted by reversed-phase HPLC. SDS PAGE and immunoblotting were used to identify the collagenous components, and N-terminal sequencing was performed to confirm these identities. RESULTS: All the synovial fluids were found to contain measurable amounts of collagen at similar concentrations. This appeared to be mainly high-molecular-weight material consisting of type I and type IX collagens, but not type II collagen. However, other smaller molecular weight type IX immunoreactive peptides were detected which were more apparent in the synovial fluids from arthritis patients. These peptides were also found to contain non-collagenous material. Collagen cross-links were also present in the arthritis synovial fluids. CONCLUSION: Collagenous material can be detected in all synovial fluids and the presence of pyridinoline cross-links indicates that at least some of this is derived from a mature collagen matrix. Type IX immunoreactive peptides were identified, but were found to contain significant amounts of non-collagenous material, and their presence, even at lower levels, in synovial fluids from normal subjects limits their potential for use as molecular markers of disease. Nevertheless, this is the first report of type IX collagen-related fragments in synovial fluids.