Background: Autoimmunity is very rare in X-linked agammaglobulinemia (XLA), although it is not common in primary antibody deficiency. Kawasaki, juvenile idiopathic arthritis (JIA) and macrophage activating syndrome (MAS) as presentation of XLA led us to report this case.Case Presentation: Our patient was a 7.5 year old boy with a history of acute flaccid paralysis. The second episode of admission, when he was 3 years old, was due to fever, generalized maculopapular rash, cervical lymphadenopathy, and bilateral non-purulant conjunctivitis (Kawasaki disease). Five months after this episode, he was admitted with prolonged arthritis and fever as a systemic onset JIA case. During 2 years, almost all drugs had been tapered and he was in remission. He was admitted again in PICU with fever, dyspnea, and pancytopenia. After some paraclinical evaluation, he was treated with IVIg and metylprednisolon plus therapy with MAS diagnosis.Similar episode plus myocarditis was repeated after 9 months. Gram negative bacilli septicemia was detected in second attack. The immune system was evaluated 1 month after the first and second episodes of MAS and low immunoglobulins and 0 level of CD19 were detected in both. XLA (Bruton) was the final diagnosis and he is on IVIg, monthly. Moreover, he is on treatment with cyclosporine, methotrexate and prednisolone for polyarthritis and he is in remission on medication now.Conclusion: XLA can be presented with various types of autoimmunity and it should be considered in a patient with several episode of autoimmunity.