Systemic lupus erythematosus (SLE) is the prototypical systemic autoimmune disease characterized by production of autoantibodies against a wide range of nuclear self-antigens. These antigens include DNA, histone and several constituents of the RNA splicing complex. Binding of autoantibodies to their specific antigens leads to tissue injury, ultimately resulting in end-organ damage. Individual SLE patients are known to have considerable variability in their specific autoantibody response patterns, and this in part correlates with their clinical manifestations. We have refined protein microarray technology and utilized it to study variation in the autoantibody response between individual SLE patients. We have further extended these studies to other diseases including primary biliary cirrhosis, rheumatoid arthritis, scleroderma, mixed connective tissue disease, multiple sclerosis, diabetes mellitus, and the myositides. Protein microarrays are produced by the application of thousands of proteins and peptides to the surface of a glass microscope slide using a robotic arrayer. We have developed an array containing the major SLE antigens including dsDNA, ssDNA, Sm, Ro, La, histones, and Sm/RNP, along with several other common disease-specific autoantigens. Arrays are probed with serum from disease or control patients, followed by incubation with fluorescently labeled, anti-human secondary antibody. Our array analysis reveals distinct autoantigen response patterns in individual SLE patients. ELISA, immunoprecipitation, and western blot analysis validate our array results. Protein autoantigen arrays represent a powerful tool which may be used to perform comprehensive studies of the breadth of epitope spreading, as well as the fine specificity of the autoantibody response. The large scale of our protein arrays allows us to examine reactivity patterns against a much wider range of autoantigens than was previously possible with more traditional methods. Our ability to distinguish autoantibody specificity patterns using autoantigen microarrays will provide further insight into the role of autoantibodies in disease progression and pathogenesis in subsets of SLE patients with distinct autoantibody responses.