The clinical utility of tissue engineering depends upon our ability to direct cells to form tissues with characteristic structural and mechanical properties across different hierarchical scales. Ideally, an engineered graft should be tailored to (re)establish the structure and function of the native tissue being replaced. Engineered grafts of such high fidelity would also foster fundamental research by serving as physiologically relevant models for quantitative in vitro studies. The approach discussed here involves the use of human mesenchymal stem cells (hMSC) cultured on custom-designed scaffolds (providing a structural and logistic template for tissue development) in bioreactors (providing environmental control, biochemical and mechanical cues). Cartilage, bone and ligaments have been engineered by using hMSC, highly porous protein scaffolds (collagen; silk) and bioreactors (perfused cartridges with or without mechanical loading). In each case, the scaffold and bioreactor were designed to recapitulate some aspects of the environment present in native tissues. Medium flow facilitated mass transport to the cells and thereby enhanced the formation of all three tissues. In the case of cartilage, dynamic laminar flow patterns were advantageous as compared to either turbulent steady flow or static (no flow) cultures. In the case of bone, medium flow affected the geometry, distribution and orientation of the forming bone-like trabeculae. In the case of ligament, applied mechanical loading (a combination of dynamic stretch and torsion) markedly enhanced cell differentiation, alignment and functional assembly. Taken together, these studies provide a basis for the ongoing work on engineering osreochondral grafts for a variety of potential applications, including those in the craniofacial complex.