Myelodysplastic syndrome (MDS) represents a group of clonal hematological disorders characterized by progressive cytopenia reflecting defects in erythroid, myeloid and megakaryocytic maturation. Cytogenetic study plays an important role in the diagnosis of chromosomal changes ranging between 23–78% have been reported in MDS patients. The authors present a case suspected to have MDS of Refractory cytopenia with multi-lineage dysplasia (RCMD)/refractory anemia with excess blasts (RAEB) -Type-1 on the bone marrow aspiration and was further studied for conventional cytogenetic analysis and deletions of 5q, 7q, 8 and 20q by and fluorescence insitu hybridization (FISH). The results of conventional cytogenetic analysis revealed t (1; 3) ((p36; q21), and FISH analysis showed a normal study for chromosomes 5, 7 and 20 suggesting that cytogenetic analysis should be performed in all MDS cases as cytogenetic analysis studies holistically all 46 chromosomes which can pick up numerical and structural anomalies and to study of micro deletions and other complex translocations it should be supplemented with FISH analysis.