Recently, the diagnosis of a variant form of chronic granulomatous disease (CGD) could be established in an 11-year-old girl who had been treated for atopic dermatitis for many years. In addition to severe superinfections of lesions of the skin, the following symptoms were found currently or in her history: an episode of chronic diarrhoea (suspected as lactose intolerance), an endomyocarditis, a paranephritic abscess and recurrent lymph node abscesses. This case is demonstrated to underline the importance of extensive immunologic diagnostics in situations of recurrent severe infections of the skin, especially if other organs are involved. Diagnosis and type of CGD were strongly indicated by flow cytometrical measurement of H2O2 and cytochrome b558-expression by neutrophils and confirmed by a Western blot test. No immunoreactive p47phox could be found in the patient's cells. In this autosomal recessive variant of CGD some retained ability of phagocytes to produce reactive oxygen intermediates was present. Special management of patients with CGD is necessary to prevent serious infectious complications. Genetic counselling is another important consequence of the correct diagnosis.