Abstract : In the last ten years, several tools have been proposed for RNA secondary structure pairwise comparison. These tools use different models (ordered tree or forest, arc annotated sequence, multi-level tree) and methods (edit distance, alignment). We present a ﬁrst benchmark for comparing these tools. For various RNA families, we built two sets of secondary structures. The ﬁrst, called the reference set, is composed of a small number of RNAs with their known structures. The second is composed of sequences folded using Mfold and RNAshapes. Some of these sequences correspond to structural RNAs of the same families (true events), other correspond to noise. We studied the ability of each tool to ﬁnd the true events using the reference set. In particular we analysed the results in terms of sensibility/speciﬁcity, distribution and spread of the scores, and computation time.