Hyper-IgM syndrome (HIM) is a rare disorder resulting from mutation in the CD40 ligand (CD40L) gene. This defect is associated with normal or elevated serum level of IgM and with low to undetectable levels of serum IgG, IgA, IgE. This case of HIM with CD40L deficiency was proven by flow cytometry but initially presented as interstitial pneumonia. Pneumocystis carinii pneumonia was highly suggested. After intravenous immunoglobulin and trimethoprim-sulfamethoxazole treatment, his lung condition improved. However, peritonitis developed and surgical intervention was performed. Ileum perforation and intestinal lymphoproliferation from a pathologic specimen were noted. Although peritonitis is extremely rare in patients with HIM, this report indicates that peritonitis which results from intestinal lymphoproliferation may be a manifestation of HIM.