The purpose of scientific visualization in chemical education is mainly to display models of static and dynamic chemical systems at a microscopic level using the results of theoretical methods. As the latter rest on various approximations, and as in addition there is little chance, if any, to compare the models with real objects, it is some sort of challenge to build and give credibility to microscopic representations when teaching a science which is essentially macroscopic. In this presentation, we shall describe how this goal may be reached by reviewing various applications we have recently developed to teach fundamental concepts in molecular structure and reactivity.