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In the elderly with cytopenia, the diagnosis of myelodysplastic syndrome (MDS) may be missed. Cytokine levels contribute to the pathology of MDS. Hence, the objectives were to evaluate cytogenetic profile as a prognostic indicator in risk stratification and cytokine levels as a screening tool in patients with cytopenia for diagnosis. Over 2 years (2016–2018), 150 elderly patients were screened. MDS diagnosis was confirmed by morphology. Interleukin-2 (IL-2) and IL-6 levels were assessed in 50 patients, and karyotyping was performed in 20 confirmed cases of MDS. Age-matched healthy controls were used for comparison of cytokine levels. Among 150 patients, 88.6% had anemia, including nutritional anemia (51.2%). MDS diagnosis was confirmed in 35 patients. In 15 patients, unexplained cytopenia (UC) was present. Karyotyping in 20 MDS patients was normal in 15 (75%) patients and revealed a complex karyotype in four (20%) patients and double chromosomal abnormality in one (5%) patient. The Revised International Prognostic Scoring System (IPSS-R) scored 91% in the low-risk group and 9% (n = 3) in the high-risk group; the latter three developed acute myeloid leukemia (AML) and two of them had a 7q deletion. Among the 15 cases of UC, one patient died from refractory anemia. No significant difference in levels of IL-2 and IL-6 were found between MDS and UC patients when compared with healthy controls, as well as between different risk groups and karyotypes. A significant difference in IL-2 levels was found in MDS patients with disease progression and with stable disease. On the basis of the findings, it is suggested that IL-2 levels will help in predicting disease progression.