Using the isomers naphthalene and azulene, and isomeric forms of the cyclohexadiene/hexatriene system, we demonstrate that the energies of Rydberg states are sensitive to the geometrical structure of the molecular ion core. Rydberg states with low quantum numbers are conveniently accessed using multi-photon excitation via valence states, providing spectra with intensity distributions that depend sensitively on the molecular isomeric form. This discovery opens up the possibility of using Rydberg states to fingerprint the shapes of molecules. Because of the large size of the Rydberg orbitals, the Rydberg fingerprint methodology can have applications in the characterization of biological and nanoscale structures. (C) 2003 Elsevier B.V. All rights reserved.