Objectives: To study the prevalence, type and etiology of anemia in newly diagnosed cases of hypothyroidism and establish a correlation between iron profile and thyroid profile of patients. Material and methods: This case control study is conducted in a y tertiary care center of southern Rajasthan and includes 100 newly diagnosed cases of hypothyroidism as cases and 100 healthy volunteers as controls. Hemoglobin, serum iron, serum ferritin and thyroid profile (T3, T4, TSH) along with peripheral smear study was evaluated in all the study participants.The results of two groups were compared and correlated using pearson’s formula. Results: Most of the study participants were from the age group 31-40 years (36.5%).Most of the study participants were female (81%).74% of cases and 16% of controls were found to have iron deficiency anemia. Peripheral smear study of the participants shows that 24% cases and 84% controls have normal study while mild microcytic hypochromic anemia was the commonest variety in cases (34%) followed by moderate microcytic hypochromic anemia (28%).Mean serum iron and serum ferritin in present study were 36.15±7.61µg/dl and 25.72±7.39 ng/ml. In present study, mean TSH of cases and controls was 19.83 ± 5.81 mIU/L and 2.86 ± 0.79 respectively. Conclusion: The prevalence of iron deficiency anemia is more common in hypothyroid patients than in general population and there exist a definite correlation between iron profile and thyroid profile.Thus, estimation of iron profile is important in hypothyroid patients for better management.