Intractable diarrhea is a major symptom of immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome and associated with autoantibodies against enterocytes. Although autoimmune enteropathy (AIE)-related 75. kDa antigen (AIE-75) is a prominent autoantigen involved in the enteropathy associated with IPEX syndrome, some patients with this syndrome demonstrated autoantibody recognizing a 95. kDa protein rather than AIE-75 in the small intestine. We, herewith, identified villin, an actin-binding protein, as the 95. kDa antigen. Four of five sera from patients with IPEX syndrome reacted with a fusion protein of glutathione-S-transferase and full length villin (GST-villin), whereas only three of 98 control sera weakly reacted with GST-villin. Anti-AIE-75 antibody was detected in all five IPEX sera but not in normal or control disease sera. We conclude that both AIE-75 and villin appear to be brush border autoantigens in IPEX syndrome and could be used for the diagnosis of AIE in patients with presumptive IPEX syndrome.