Stem cells are self-renewing cells that can be differentiated into other cell types. Conventional in vitro models for studying stem cells differentiation are usually preformed in two-dimensional (2D) cultures. The design of three-dimensional (3D) in vitro models which ideally are supposed to mimic the in vivo stem cells microenvironment is potentially useful for inducing stem cell derived tissue formation. Biodegradable scaffolds play an important role in creating a 3D environment to induce tissue formation. The application of scaffolding materials together with stem cell technologies are believed to hold enormous potential for tissue regeneration. In this review, we provide an overview of application of tissue engineered scaffolds and stem cells for the development of stem cell-based engineered tissue replacements. In particular, we focus on bone marrow stem cells (BMSCs) and mesenchymal stem cell (MSCs) due to their extensive clinical applications.