Selective per-substituted cyclodextrin design enables the carrier's physicochemical and binding properties to be tailored and can even modify some biological native structure effects. We herein report a number of highly efficient microwave-assisted synthetic protocols for the preparation of several amino, ureido and thioureido per-substituted β-cyclodextrin derivatives. A rapid parallel synthetic approach has given a set of 14 different CD derivatives. Our strategy is supported by computational analyses which were used to estimate the physicochemical behaviour of per-substituted derivatives and to tailor suitable substituents.