Autoimmune hepatitis (AIH) is a chronic necroinflammatory disease of the liver with a poorly understood etiology. Detection of non-organ-specific and liver-related autoantibodies using immunoserological approaches has been widely used for diagnosis and prognosis. However, unambiguous and accurate detection of the disease requires the identification and characterization of disease-specific autoantigens. In the present study, we have used protein microarray technology to profile the autoantigen repertoire of patients with AIH versus those with other liver diseases, identifying and validating novel and highly specific biomarkers for AIH. Using two algorithms developed in the current study, we were able to demonstrate that a panel of six autoantigens could be used in combination to clearly diagnose AIH-positive serum samples.