SUMMARYCryptosporidium sp is a protozoan that displays an intracellular settlement primarily in the intestinal systems of humans and can result in diarrhoea. Undernourished children and persons with immunosuppression in developing countries are especially vulnerable to infection with this parasite. A 12-month-old female presented at Ege University, Faculty of Medicine, Department of Paediatrics with complaints of fever, diarrhoea, respiratory distress and growth-development retardation was diagnosed with CD40 deficiency (Hyper IgM Type 3). During the one year investigation process of the case with chronic diarrhoea and necrotic pneumonia, Cryptosporidium sp oocysts were found in nine of the 22 faecal examinations and also in transtracheal aspiration liquid examined using the Kinyoun Acid-fast staining method. In conclusion, it is thought that cryptosporidiosis should also be considered in the distinct diagnosis of immunodeficient infants who are presented with respiratory and gastrointestinal system complaints.