RNA tertiary motifs play an important role in RNA folding. To understand the complex organization of RNA tertiary interactions, we compiled a dataset containing 54 high-resolution RNA crystal structures. Seven RNA tertiary motifs (coaxial helix, A-minor, ribose zipper, pseudoknot, kissing hairpin, tRNA D-loop:T-loop and tetraloop-tetraloop receptor) were searched by different computer programs. For the non-redundant RNA dataset, 601 RNA tertiary interactions were found. Most of these 3D interactions occur in the 16S and 23S rRNAs. Exhaustive search of these motifs revealed diversity of A-minor interactions, and other loop-loop receptor interactions similar to the tetraloop-tetraloop receptor. Correlation between motifs, such as pseudoknot or coaxial helix with A-minor, shows that they can form composite motifs. These findings may lead to tertiary structure constraints for RNA 3D prediction.