Despite recent advances in medicine and surgery, many people still suffer from cardiovascular diseases, which affect their life span and morbidity. Regenerative medicine and tissue engineering are novel approaches based on restoring or replacing injured tissues and organs with scaffolds, cells and growth factors. Scaffolds are acquired from two major sources, synthetic materials and naturally derived scaffolds. Biological scaffolds derived from native tissues and cell-derived matrix offer many advantages. They are more biocompatible with a higher affinity to cells, which facilitate tissue reconstruction. Interestingly, xenogeneic recipients generally tolerate their components. Therefore, heart valve tissue engineering is increasingly benefiting from naturally-derived scaffolds. In this review, we investigated the different protocols and methods that have been used for heart valve decellularization.