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Myelodysplastic Syndromes (MDS) are heterogeneous group of myeloid malignancies that result in bone marrow failure and peripheral blood cytopenias. Elliptocytes are most abundant in hereditary elliptocytosis. Isolated deletion 20q [del (20q)] associated with elliptocytosis in a patient of myelodysplastic syndrome is very rare and only few cases are reported in literature. We report a case of 72 year old male presented with thrombocytopenia and anaemia and marked RBC elliptocytosis, diagnosed as refractory anaemia with multilineage dysplasia associated with isolated del (20q) on FISH analysis of bone marrow. The presence of cytogenetic alterations have diagnostic and prognostic role. Deletion of the long arm of chromosome 20 [del (20q)] may be an early and primary genetic event in several haematological disorders. Chromosome 20q deletion is associated with about 5% of primary MDS.