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CD40 deficiency yield to an autosomal recessive subtype of hyper-immunoglobulin M syndrome (HGIM type 3), presenting with an almost identical clinical picture to X-linked CD40L deficiency (HIGM type 1) with profound T-cell dysfunction yielding to opportunistic infections as well as neutropenia, autoimmunity, and malignancy. We presented a girl with recurrent upper respiratory tract infections and lymphoid hyperplasia which was diagnosed with type 3 hyper IgM syndrome due to CD40 gene mutation. Otitis media with opportunistic germs and no evidence for an X-linked pattern of inheritance were diagnostic keys to type 3 hyper IgM syndrome in our patient.