Problems involving physiochemical phenomena on both the microscopic and macroscopic scales often raise similar sets of generic issues and questions. The complexity of these problems is beginning to make inoperative the traditional intuition-based approaches to their analysis and solution. The common characteristics of large, multivariable, complex molecular systems call for a new, more systematic approach to guide theoretical and experimental efforts. With mathematical modeling becoming an essential ingredient in the studies, it is argued that molecular systems analysis and especially the systematic tools of sensitivity analyis can play an increasingly important role in understanding and finding solutions to complex, chemically based problems.