Mineralocorticoids play a major role in regulating sodium and potassium homeostasis and also contribute to the control of blood pressure and in some physiological disorders. The physiological effects of this class of corticosteroids are mediated by ligand-induced nuclear transcription factor, the mineralocorticoid receptor(MR)/glucocorticoid receptor(GR), a member of the steroid/nuclear receptor superfamily. Although the MR interacts with both glucocorticoids and mineralocorticoids, the GR interacts specifically with glucocorticoids. The three dimensional structure of progesterone complexed to its receptor revealed in X-ray diffraction method is utilised to develop a homology model of human mineralocorticoid receptor ligand binding domain (hMR LBD) in a similar fashion as mouse GR LBD was developed previously. The secondary structure of hMR LBD contains eleven helices, eight turns and four sheets. This receptor contains a long helix, H9, with thirty four residues. The 12-residue C-terminal extension (residues 973–984) of hMR LBD, which is essential for hormone binding, is tightly fixed in position by an antiparallel β-sheet interaction. The three dimensional model reveals two polar sites located at the extremities of the elongated hydrophobic ligand-binding pocket (LBP). De-oxy corticosterone (DOC) is docked to the LBP's of both hMR LBD and mGR LBD. The difference accessible surface area (DASA) study revealed the interaction zones of both the receptors in complex with DOC. Observations relating to the native and complex proteins revealed a close structural kinship between hMR LBD and mGR LBD.