Secondary pulmonary alveolar proteinosis (PAP) is a rare lung disease that has been reported in 13 cases of myelodysplastic syndromes (MDS). A dicentric isochromosome of deleted chromosome 20q, idic(20q–), is a newly recognized rare, but recurrent, cytogenetic anomaly that has been described in 28 cases of MDS. Recently, we encountered an interesting MDS patient with idic(20q–) and secondary PAP. At presentation, she was a 40-year-old woman with pancytopenia and dysplasia involving 2 cell lineages that were compatible with refractory cytopenia with multilineage dysplasia. A chromosome analysis of bone marrow cells using the R-banding technique revealed a karyotype of 46,XX,–20 and +a small metacentric marker chromosome. Fluorescence in situ hybridization demonstrated this marker chromosome to be idic(20q–). Three years after presentation, her disease was complicated by secondary PAP that was confirmed by chest computed tomographic scans and a thoracoscopic lung biopsy, revealing the characteristic periodic acid Schiff stain-positive materials filling the alveoli. The patient subsequently died of respiratory failure 45 months after diagnosis. To our knowledge, this is the first MDS patient with idic(20q–) and secondary PAP to be reported in the literature. Moreover, this patient is also the 29th MDS case with idic(20q–).