The calculation of reliable alignments for structured RNA is still considered as an open problem. One approach is the incorporation of secondary structure information into the optimization criteria by using a weighted sum of sequence and structure components as an objective function. As it is not clear how to choose the weighting parameters, we use multi-objective optimization to calculate a set of Pareto-optimal RNA sequence-structure alignments. The solutions in this set then represent all possible trade-offs between the different objectives, independent of any previous weighting.