Advancements in biomaterials and stem cell technology have lead current medical technology to tissue engineering and regenerative medicine. Human engineered cartilage, bone, fascia, tendon, nerve and skin tissues have been used for the treatment of tissue injuries and degenerative diseases in combination with embryonic, fetal or adult stem and progenitor cells. Mesenchymal stem cells are one of the most extensively studied adult stem cell population and are widely utilized in cell therapies. Regeneration and 3-dimensional reconstruction of specialized connective tissues by combining differently originated micro and nanoscaled, natural or synthetic scaffolds with stem or progenitor cells are highly expected to guarantee patients to maintain acceptable life quality. In this review we discuss the important issues in biomaterial and stem cell interactions based on histological biocompatibility, updating recent basic research in this field and addressing possible future perspectives.