Abstract Summary: Incorporating secondary structure information into the alignment process improves the quality of RNA sequence alignments. Instead of using fixed weighting parameters, sequence and structure components can be treated as different objectives and optimized simultaneously. The result is not a single, but a Pareto-set of equally optimal solutions, which all represent different possible weighting parameters. We now provide the interactive graphical software tool RNA-Pareto, which allows a direct inspection of all feasible results to the pairwise RNA sequence-structure alignment problem and greatly facilitates the exploration of the optimal solution set. Availability and implementation: The software is written in Java 6 (graphical user interface) and C++ (dynamic programming algorithms). The source code and binaries for Linux, Windows and Mac OS are freely available at http://sysbio.uni-ulm.de and are licensed under the GNU GPLv3. Contact: [email protected]