Traditional approaches in measuring the effi cacy of antimicrobials, antivirals, antifungals, and antiparasitic therapies have limitations which contribute to noise in effi cacy assessment. These include the following: (1) large number of animals must be sacrifi ced at multiple time points to assess the effects of therapy on pathogen titers in the organs; (2) weight loss of 25-30 % in animals requires ethical animal euthanasia which may be unscheduled and skew sampling; and (3) the organ titers are based upon ex vivo culture or analysis. Such limitations can lead to erroneous conclusions regarding drug effi cacy versus spontaneous recovery. One needs to evaluate dissemination of the pathogen in vivo within the same animal to truly measure effi cacy. Bioluminescence imaging (BLI) has been developed as a new method to monitor infections in small animal models. BLI is based on noninvasive measurement of biomarkers possessing a light-producing luciferin or other light-emitting metabolic substrates. This imaging platform is now a widely used technique in oncology, tumor metastasis, establishing effi cacy of anticancer and anti-infective therapies, detecting protein-protein interactions, detecting transgene expression in vivo, and many more. BLI, importantly, enables each animal to be used as its own control over time, thus limiting the number of animals required in studies and minimizing animal-to-animal variations which improves statistical precision of effi cacy outcomes. In this chapter we describe applications of BLI in the study of infection, reveal important limitations of the technique, and summarize recent work in murine microbial and viral models.