A 51-year-old man with myelodysplastic syndrome (MDS) was admitted to our hospital because of dyspnea on exertion in December 1999. Chest radiography showed ground-glass shadows in the middle and lower fields of both lungs, and chest computed tomography revealed a typical "crazy paving appearance". The bronchoalveolar lavage fluid was milky in appearance, and so secondary pulmonary alveolar proteinosis associated with MDS was diagnosed. Because there was no need to treat his MDS, we twice performed whole-lung lavage under general anesthesia in January and February 2000. The treatments were effective, and his abnormal chest radiography findings, laboratory data and pulmonary function were normalized. This was a rare case of secondary pulmonary alveolar proteinosis associated with MDS successfully treated with whole-lung lavage.