Pathogens exhibit remarkable abilities to flout therapeutic intervention. This outcome is driven by evolution, either as a direct response to intervention (e.g. the evolution of antibiotic resistance), or through long-term coevolution generating host or parasite traits that interact with therapy in undesirable or unpredicted ways. To make progress, the concepts and techniques of evolutionary biology must be deeply integrated with traditional approaches to immunology and pathogen biology. An interdisciplinary approach can inform control strategies, or even patient treatment, positioning us to meet the current and future challenges of controlling infectious diseases.