Bloody stools, diarrhea and perianal abscesses were observed from the age of two months infant. The boy received a BCG vaccination at the age of four months. The patient was diagnosed as having Crohn's disease at the age of six months by intestinal endoscopy. Based on the diagnosis, he was treated with nutrition therapy, salazosulfapyridine, and prednisolone. Fever of unknown origin occurred two months after he had taken azathioprine at the age of two years and two months. Mycobacterium tuberculosis was detected from a gastric aspirate, and he was diagnosed as having disseminated BCG infection by means of the multiplex PCR method. Chest CT showed miliary pulmonary nodules in both lungs on admission. Physical examination revealed enlarged lymphnodes, which were palpable around the neck and groin, and hepatomegaly. Laboratory data were within normal ranges except a slightly increased peripheral white blood cell and serum CRP level. He was treated with rifampicin (15 mg/kg/day), isoniazid (15 mg/kg/day) for 12 months, and streptomycin (25 mg/kg/day) for two months. He became afebrile a week after starting the treatment, and the miliary pulmonary nodules in both lungs had disappeared by 5 months after starting the treatment. An abnormality of the NEMO gene, which is the gene responsible for ectodermal dysplasia and immunodeficiency, was identified at the age of three years. It is assumed that an abnormality of the NEMO gene caused a latent BCG infection over a period of one year and ten months, and immunosuppressive medicine (azathioprine) induced a disseminated BCG infection. This case report supports that anti-tuberculosis medicine should be given to prevent disseminated BCG infection if an infant who receive immunosuppressive therapy is found to have an immune deficiency characterized by a mycobacterium infection after BCG vaccination.