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Background: Eosin-5-Maleimide (EMA)-based flow cytometry binds to red blood cell (RBC) membrane-associated proteins which can be used to detect red blood cell (RBC) membrane disorders. Myelodysplastic syndromes (MDS) are stem cell disorders resulting in ineffective hematopoiesis which is commonly present with anemia and erythroid dysplasia. Objectives: We aimed to study RBC membrane defects in MDS using flow cytometry for EMA staining. Methods: We enrolled anemic patients who were diagnosed with low-risk MDS (R-IPSS score ≤ 3.5), RBC membrane disorders [hereditary spherocytosis (HS) and Southeast Asian ovalocytosis (SAO)], and normal controls. Complete blood count (CBC) and flow cytometry for EMA staining were performed. Results: There were 16 cases of low-risk MDS, 6 cases of RBC membrane disorders, and 15 control cases. Mean fluorescence intensity (MFI) of EMA binding test in the RBC membrane disorders was significantly lower than controls (17.6 vs. 24.3, p < 0.001), but the EMA binding test in the low-risk MDS was not significantly different than the controls (26.5 vs. 24.3, p = 0.08). Conclusion: the RBC membrane defect in low-risk MDS was not demonstrated as having detection ability using EMA binding test with flow cytometry.