Even though autoimmune diseases are heterogeneous, believed to result from the interaction between genetic and environmental components, patients with these disorders exhibit reproducible patterns of gene expression in their peripheral blood mononuclear cells. A portion of this gene expression profile is a property of familial resemblance rather than autoimmune disease. Here, we wanted to identify the portion of this gene expression profile that is independent of familial resemblance and determine whether it is a product of disease duration, disease onset or other factors. By employing supervised clustering algorithms, we identified 100 genes whose expression profiles are shared in individuals with various autoimmune diseases but are not shared by unaffected family members of individuals with autoimmune disease or by controls. Individuals with early disease (1 year after onset) and established disease (10 years after onset) exhibit a near-identical expression pattern, suggesting that this unique profile is a product of disease onset rather than disease duration.