Biological systems including cells and tissues in living bodies are complex, hierarchical, and dynamic, and they always inspire us to design materials for possible applications. These structures are basically constructed from the appropriate building blocks via various intermolecular forces such as van der Waals interactions, hydrogen bonds, electrostatic interactions, and sometimes hydrophobic effects in water, and are directly adapted to performing a variety of functions such as intercellular signal transduction through plasma membranes, intracellular metabolism triggered by cytoplasmic calcium increase, and cellular proliferations [1, 2]. In the last quarter of a century, many scientists have studied interfacial phenomena between these biological systems and surfaces of artificial materials in order to design functional biomaterials for medical uses. Throughout these researches, it has been well recognized that biological responses to these surfaces include complicated acute and chronic reactions, eventually leading to cellular and tissue rejection in living bodies. In order to solve these problems, one must understand and appreciate any differences with respect to the structures and their functions between natural tissues and artificial materials. From this point of view, it should be stated that one of the dominant differences would be the mobility of molecules constructing these materials, and a quite new approach is urgently required to design biomaterials which can perform new functions in future advancing medicines.With this in mind, we initiated a study of cyclodextrin (CD)-based polyrotaxanes as novel biomaterials, because CD molecules would be expected to move along the polymeric chain. One of the characteristics seen in polyrotaxanes is the mobility of cyclic compounds, and they can be freely rotational and sliding if any intermolecular forces with the linear chain and the neighboring cyclic compound are eliminated (Figure 9.1). In particular, polyrotaxanes consisting of a-CD molecules and a poly (ethylene glycol) (PEG) [3, 4] chain are possible biomaterials in the structural components, as a-CD and PEG have been approved by the FDA for use in foods and drugs. We have prepared biological ligand-conjugated polyrotaxanes and Supramolecular Polymer Chemistry, First Edition. Edited by Akira Harada.