The invention relates to methods and materials involved in diagnosing and treating autoimmune conditions. In particular, the invention relates to methods and materials involved in diagnosing arthritis conditions that are accompanied by an NADPH oxidase deficiency, methods and materials involved in treating, preventing, or delaying the onset of arthritis conditions that are accompanied by an NADPH oxidase deficiency, and methods and materials involved in identifying agonists and antagonists of NADPH oxidase activity.