The protozoan Cryptosporidium affects the digestive tract of humans and animals. Cryptosporidiosis leads to diarrhoea mimicking a cholera-like course with dehydration and may even result in death in immunodeficient patients, as patients with hyper-IgM syndrome. We describe a rare case of disseminated Cryptosporidium infection in a seven- year-old boy with CD40 L deficiency. During the pre-graft phase, the patient presented an intestinal cryptosporidiosis which became complicated few days later during the aplasia period with a cholangitis and pulmonary cryptosporidiosis. Cryptosporidium hominis was identified. After treatment with nitazoxanide and azithromycine the patient was doing well.