PFAPA syndrome is a chronic disease classified in the group of autoinflammatory syndromes characterized by periodic fever, aphthous stomatitis, pharyngitis, and cervical adenitis in young children. The etiology of this disorder is still unknown, but a primary dysfunction of the innate immune system seems to be involved. According to Marshall criteria, it is not possible to diagnose PFAPA in the presence of autoimmune diseases. We present here the case report of an 8-month girl with PFAPA who developed autoimmune hepatitis type 2 at the age of 18 months. We suppose that the dysregulation in innate immunity that is typical of patients with PFAPA could trigger autoimmune disorders such as autoimmune hepatitis in susceptible subjects. The possible relationships between immune-system dysfunction peculiar to this syndrome and autoimmune hepatitis are discussed.