Flow cytometry (FCM) is a reproducible and objective technique that may be useful in the diagnosis of myelodysplastic syndrome (MDS) by detecting abnormal immunophenotypes specific to MDS. We investigated 5 granulocyte/monocyte panels by FCM to find a sensitive and specific combination of panels in order to discriminate MDS from non-clonal hematologic disorders. Bone marrow aspirates from 35 patients with MDS and 25 patients with non-clonal hematologic disorders were studied. We performed FCM using 5 granulocyte/monocyte panels (CD15/CD10/CD45, CD64/CD33/CD45, CD16/CD13/CD45, CD16/CD11b/CD45, and CD56/CD19/CD7/CD45) to examine the positive rate in MDS and controls, and to find an optimal combination that maximizes the detection rate of MDS. In MDS, the number of abnormal immunophenotypes per 5 granulocytic and 5 monocytic panels were 2.1 ± 1.2 and 2.2 ± 1.4. The rates were higher than the controls (P< 0.001, respectively). As the number of employed panels increased, the percent values of abnormal immunophenotypes increased (P=0.002). The maximum rate of abnormal immunophenotype was 89.7% in MDS patients, especially 100.0% in normal karyotype, when a combination of three panels, CD15/CD10/CD45, CD64/CD33/CD45, and either CD16/CD13/CD45 or CD16/CD11b/CD45 was used. This study demonstrates that a combination of CD15/CD10, CD64/CD33, CD16/CD13 or CD11b granulocyte panels in FCM is sensitive and specific for diagnosis of MDS.