The need for new antifungal agents continues, fueled by opportunistic infections in immune-compromised patients and by the development of resistance to existing agents. Natural products offer a virtually unlimited source of unique molecules and not only serve as a reservoir for new potential drugs and drug prototypes, but also for probes of fungal biology. In this chapter, whole-cell screening methods targeted for natural products are illustrated, including general microplate-based screening, bioautography, and mode of action studies, including the use of genetically altered fungal strains now available commercially.