A male infant exhibited thrombocytopenia at birth, and later developed leukocytosis, monocytosis, and bloody stool. The bone marrow was hypercellular with dysplasia. Spontaneous granulocyte/macrophage-colony formation and hypersensitivity to granulocyte/macrophage-colony stimulating factor were confirmed by in vitro culture. These findings fulfilled most of the diagnostic criteria for juvenile myelomonocytic leukemia (JMML), with the exception of splenomegaly. However, no mutations in the PTPN11, RAS, and CBL genes, or clinical features of neurofibromatosis type 1, which are associated with JMML, were detected. The patient subsequently developed refractory eczema with undetectable serum IgM, which led to the consideration of Wiskott-Aldrich syndrome (WAS). Lack of WASP expression and a 4-nucleotide deletion mutation in WASP were identified. Approximately 20 % of patients with JMML show none of the abovementioned molecular abnormalities. Careful differential diagnosis, including the consideration of WAS, is, therefore, recommended in patients with clinical features and laboratory findings consistent with JMML.