Computer-based visualizations play a profoundly important role in chemistry instruction. In this chapter, we review the role of visualization tools and possible ways in which they may influence thinking about chemistry. There are now several visualization systems available that allow students to manipulate important variables in obtain a solution to a scientific problem. We discuss the fundamental differences between these tools, and we emphasize the use of each within the context of constructivist curricula and pedagogies. We also consider the impact such tools may have on visuo-spatial thinking. We suggest that although visuo-spatial ability may be important in visualization use, its role has at times been overemphasized. We argue for a more nuanced, richer understanding of the many ways in which visuo-spatial reasoning is used in solving chemistry problems. This discussion leads to a set of design principles for the use of visualization tools in teaching chemistry. Finally, we present our work on the Kinemage Authorship Project, a program designed to assist students in understanding spatial structures in complex, biochemical molecules. The Kinemage Authorship Project allows students to construct their own molecular visualizations, and we discuss how this may lead to greater understanding of the spatial properties of molecules. This constructivist program embodies many of the design principles that we present earlier in the chapter.