Serious hematological diseases often cause respiratory disorders. Because these are related to the prognoses of patients with hematological diseases, their early diagnosis is necessary. This study describes a 6-year-old girl with myelodysplastic syndrome complicated by pulmonary alveolar proteinosis who showed a remarkable increase in her serum KL-6 level. Three years and 2 months after the end of therapy for neonatal melanoma, a diagnosis of myelodysplastic syndrome with leukemic change was made. Ten months after the onset of leukemia, she had respiratory distress with an increased serum KL-6 level of 75,000 U/mL (reference range; < 500 U/mL). Despite various treatments for pulmonary complications, she died 3 months after developing respiratory distress. A diagnosis of pulmonary alveolar proteinosis was made at autopsy. Earlier treatment of respiratory distress could be achieved if serum KL-6 levels were examined earlier.