We describe a molecular construction kit in which amphiphilic polymers and functionalized cyclodextrins are arranged into sophisticated molecular architectures in aqueous solution without the need to perform chemical reactions. Therefore, these systems are highly biocompatible and show programmable lifetimes. The kinetic stabilities of our polyrotaxane structures are tunable using sterically demanding groups that hinder dissociation. These cyclodextrin-based polymer systems are applicable in principle for the detection of analytes at the level of single molecules. These systems may also serve well in targeted drug delivery and gene transfection. (C) 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47:6333-6341, 2009