Hyperthyroidism due to certain types of thyroiditis which can eventually lead to hypothyroidism as the thyroid gland is damaged. Also, radioiodine treatment of Graves' disease often eventually leads to hypothyroidism. Such hypothyroidism may be treated by regular thyroid hormone testing and oral thyroid hormone supplementation. In this research work we identify the potential protein targets of the Thyroid hormone receptors of Human beings and Rat. Bioinformatics software and tools are used to analyze the protein sequence and structure. Our primary idea is to show how the sequence and 3D structures share homology on a molecular basis. The results of Insilico studies clearly show that the Rat –Thyroid hormone receptor can act as a potential agent for testing protocols and clinical studies for novel drug candidates.