Matrix metalloproteinase 20 (MMP20, enamelysin) protein encoded by Matrix metallopeptidase 20 (MMP20) gene, found in developing tooth enamel is believed to organize enamel crystals during tooth development by acting as a crystallization centre for mineralization. During enamel formation, in absence /malfunction of this protein, amelogenin and other proteins are not cleaved properly. Thus, enamel becomes soft, rough, discolored and prone to breakage because of abnormal crystal structure (Amelogenesis imperfecta). The motive of the present study was to predict the 3-D structure of human Mmp-20 using computational methods. Homology modeling was carried out using PDB Blast, followed by threading and ab-initio structure prediction techniques to obtain the protein model which was further refined, optimized and analysed using different bioinformatics servers and softwares. The model obtained from I-Tasser was selected and further refined by loop using MODELLER 9v7 and optimized. On analysis, it gave an acceptable Procheck, Verify-3D and Errat results. This model can be used to check interaction with protein amelogenin that is responsible for its proteolysis resulting in normal mineralizationin tooth enamel. This study can be helpful in enhancing our knowledge about this process occurring in humans which has been studied mostly in pigs and can lead to formulation of new restorative and more biocompatible materials.