A method has been developed for predicting the tertiary structures of RNA-RNA complex structures using secondary structure information and a fragment assembly algorithm. The linker base pair and secondary structure potential derived from the secondary structure information are particularly useful for prediction. Application of this method to several kinds of RNA-RNA complex structures, including kissing loops, hammerhead ribozymes, and other functional RNAs, produced promising results. Use of the secondary structure potential effectively restrained the conformational search space, leading to successful prediction of kissing loop structures, which mainly consist of common structural elements. The failure to predict more difficult targets had various causes but should be overcome through such measures as tuning the balance of the energy contributions from the Watson-Crick and non- Watson-Crick base pairs, by obtaining knowledge about a wider variety of RNA structures.