Chemoinformatic approaches have an essential role in the systematic description and visualization of the chemical space for drug discovery projects. These methods enable the quantitative comparison of general screening collections and the systematic classification of approved drugs and databases annotated with biological activity to define biologically and medicinally relevant chemical spaces. Profiling of chemical diversity, molecular complexity, and physicochemical properties of compound libraries using chemoinformatic approaches provide a solid basis to generate hypothesis of how to interrogate novel areas of chemical space for enhanced drug discovery. This commentary is focused on the application of chemoinformatic approaches to mine, and to navigate the chemical space of compound collections. The discussion is centered on the concept of chemical space, types of compound libraries used in drug discovery programs, applications of chemical space mining and visualization using chemoinformatic methods, and strategies to expand the pharmaceutical relevant chemical space with emphasis on the notion of molecular complexity.