Though deceptively simple to teach, chromatography presents many nuances and complex interactions that challenge both student and instructor. Time and instrumentation provide major obstacles to a thorough examination of these details in the laboratory. Modern chromatographic method-development software provides an opportunity to overcome this, presenting a valuable extension to existing lectures and laboratory sessions. This article describes the pedagogical goals and objectives, as well as the successful implementation, of two virtual laboratory exercises in an undergraduate separation-science course. These differ from conventional simulations in that the user can vary chromatographic parameters while directly observing their effect on the chromatogram without waiting for the latter to "develop". These self-paced independent-learning activities give students an improved understanding of the molecular basis of separation in chromatography, reinforcing the connections with fundamental chemical principles. Finally, such software provides an opportunity to include topics not covered in typical undergraduate texts, but of great importance to contemporary chromatography. These include the concept of robustness, the use of resolution maps, and the significant role of pH in controlling both resolution and elution order in HPLC. (Contains 5 tables and 5 figures.)