In this Letter, based on chaos game representation (CGR), we propose a 3D graphical representation for RNA secondary structures in terms of classifications of bases of nucleic acids. Some information on the base distribution and compositions of RNA secondary structure can be intuitively reflected by the graphical representation. Furthermore, the numerical characterization of the graphical representation is applied to compute the similarities of RNA secondary structures. As application, we make quantitative comparisons for two sets of RNA secondary structures based on the graphical representation. (c) 2008 Elsevier B.V. All rights reserved.