In this Letter, we propose a relatively simple measure to compare RNA secondary structures. We first transform an RNA secondary structure into number sequences differentiating paired bases from free bases of the RNA molecule. Then, based on a new 2D graphical representation of the number sequence, we can obtain the relative distance and the relationship tree of RNA secondary structures. The examination of similarities/dissimilarities of two sets of RNA secondary structures illustrates the utility of the approach. Unlike most existing comparison approaches, our scheme considers the different roles of free bases and paired bases in stabilizing RNA secondary structures, and clearly represents the paired regions and free bases of RNA in 2D graph. (C) 2008 Elsevier B.V. All rights reserved.