For a number of years I have been interested in applying high-throughput genomic approaches to the study of autoimmune disease. Most recently I have been involved in the establishment of the Cambridge Hinxton Centre for Translational Research in Autoimmune Disease. This is a collaboration between clinicians, basic scientists and bioinformaticians that aims to apply expression profiling to the clinical management of autoimmune diseases such as systemic lupus erythematosus and small vessel vasculitis. We have developed and optimised a cell selection strategy that enables us to expression profile purified leukocyte subsets isolated from patients with active disease pre- and post-treatment. This should enable the development of novel biomarkers that can be used to stratify patients at presentation, select appropriate treatment protocols, monitor response and predict relapse. In addition, it may also provide insight into the molecular pathogenesis of disease.