Microbicides, substances applied topically to prevent sexual HIV infection, are needed to empower receptive sexual partners with effective prevention methods. Several large microbicide trials, however, failed to demonstrate efficacy, thus motivating a reevaluation of the current microbicide development paradigm, which has been largely empirically based. Microbicide use occurs in a highly complex environment involving multi-level interactions, behavioral and biochemical, among host, virus, and drug, yet many details of these interactions remain unknown. Fundamental information regarding virus and drug distribution over time in sexually receptive body compartments that is necessary to design a microbicide able to outdistance and outlast the virus is largely absent. Recent efforts have been made to establish a simple conceptual framework for obtaining the knowledge that is likely to inform a more mechanistic, model-based development paradigm. These efforts have also advanced the development of numerous methodological approaches to obtain the knowledge needed to improve microbicide development.