Computing the surface of a molecule (e.g., a protein) plays an important role in the analysis of its geometric structure as needed in the study of interactions between proteins, protein folding, protein docking, and so forth. There are a number of algorithms for the computation of molecular surfaces and their triangulations, but only a few take advantage of graphics processing unit computing. This paper describes a graphics processing unit-based marching cubes algorithm to triangulate molecular surfaces. In the end of the paper, a performance analysis of three implementations (i.e., serial CPU, CUDA, and OpenCL) of the marching cubes-based triangulation algorithm takes place as a way to realize beforehand how molecular surfaces can be rendered in real-time in the future. Copyright © 2011 John Wiley & Sons, Ltd.