Background: Primary acute malnutrition in children is the result of inadequate food supply caused by socioeconomic, political, and environmental factors, and it is most commonly seen in low- and middle-income countries. There are marked change in secretion and metabolism of thyroid hormones and in structure of thyroid gland in PEM. There is limited data and studies available regarding concentration of FT3 and FT4 levels in PEM children. Method: A Prospective observational Study done at rural tertiary care hospital. 100 Out of 112 children in the 6 months to 60 months of age diagnosed as PEM were analysed for the study during 2 years and 4 months. Study participants were divided on the basis of WHO staging for acute malnutrition. Detail clinical assessment of nutritional status was carried out along with history and anthropometric measurement in case Performa. Thyroid function test and Serum proteins was done. Statistical Analysis was performed. Results: In our study a very highly significant correlation noted between low FT3 and type of malnutrition. The mean FT4 value in children with SAM was less than children with MAM. The difference between the two groups of cases was found to be statistically highly significant (p<0.001).We observed that there was no correlation between TSH values and the type of malnutrition. The mean serum proteins, albumin and globulin were significantly lower and a positive correlation with type of malnutrition. A/G ratio was decreased in both SAM and MAM children and highly significant correlation with low FT3. FT4 had a significant correlation with decreased A/G ratio. There was no significant relation between the A/G ratio and TSH. Conclusion It is also important to bear in mind whether total (TT4, TT3) or free (FT4, FT3) Thyroid Hormone are measured, as changes in circulating binding proteins can seriously confound interpretation of TT4 and TT3 concentrations.