Present review article emphasizes role of biological scaffolds, hydrogels and stem cells in tissue engineering mainly in regeneration or repairing of damaged tissues. Highly porous scaffold biomaterials are developed which act as templates for tissue regeneration and potentially guide the growth of new tissue. Present article also describes de-cellularization, cell printing, vascularization, integration of cross linking of methods for scaffolding of biomaterials to reproduce and recapitulate complexity in engineered tissues. It also explains different scaffold types, polymer hydrogels which are necessary for formation of microstructure, cell attachment, differentiation, tissue vascularization and integration. It also explains use of induced pluripotent stem cells (iPSCs) and engineered MSCs as new diagnostic and potential therapeutic tools to remove sustained damage and complications from organ failures. These engineered MSCs assist in making self-assembling supramolecular hydrogels, which have larger applications in cell therapy of intractable diseases and tissue regeneration. No doubt development of more advanced biomaterials, growth factors and stem cell derived products/factors and tissue transplantation methods based on cell regeneration programming will revolutionize the clinical therapeutics. This article suggests identification of new biomaterials/biomolecules such as growth factors, scaffolds, integration, adhesion and regulatory molecules and cell secreted factors which can induce major metabolic and signaling pathways during phase of tissue repairing and induction of regeneration. This innovative research area needs many conceptual improvements in organ therapies, methods and technological advancement to scale more services to the human society.