Intercropping, the simultaneous cultivation of multiple crop species, has been used throughout history and remains common among farmers of small landholdings in the tropics. One benefit of this practice may be disease control. In phenomenological research comparing disease in monocrops and intercrops, primarily due to foliar fungi, intercropping reduced disease in 73% of more than 200 studies. Nematodes are the primary pathogen for which disease increases are reported, but variability in disease impacts among studies can be high for all types of diseases. The mechanisms by which intercrops affect disease dynamics include alteration of wind, rain, and vector dispersal; modification of microclimate, especially temperature and moisture; changes in host morphology and physiology; and direct pathogen inhibition. The effect of intercropping on host density is a factor underlying many of these mechanisms. By synthesizing our growing understanding of mechanisms and their interactions with phenomenological studies, we may develop a theoretical grounding that allows us to improve the application of intercropping for tropical smallholders and industrial farmers alike.