There is disclosed a method for visualizing secondary structures of RNA molecules, by which nearly overlap-free polygonal displays of RNA secondary structures are produced with minimal distortion to structural elements, with minimal search for positioning them, and with minimal user intervention. While vector and vector space are used to determine the direction and space of a structural element, two heuristics are adopted for the task of searching for the space and direction of structural elements. With the aid of the two heuristics, loops are positioned in decreasing order of their sizes and a helix is positioned, depending on the position of its adjacent loop which has been positioned. In consideration of both a potentially open and wide vector space and an allowed vector space, a structural element is positioned.