For years, great efforts have been made by scientists to construct various novel interlocked supramolecular systems. A wide range of pseudorotaxanes and rotaxanes, full of challenging constructions and potential applications in areas such as nanostructured functional materials, molecular switches, molecular logic gates, molecular wires, memory devices Willner and biomedical applications have been reported recently. Cyclodextrin polyrotaxantes or polypseudorotaxanes there are not only nice and interesting supramolecular architectures but they also have a high interest for biomaterials application that allow to opened up new approaches for tissue regeneration, drug and gene delivery. The use of the supramolecular cyclodextrins complexes has given rise to interesting studies to design and develop new biomaterials with advanced properties. In this review we will update the recent advances in the use of CDs-supramolecular structures for develop new and advanced drug and gene delivery systems and for use in tissue engineering.