We studied the relationship between genetic diversity and disease susceptibility in honey bee colonies living under natural conditions. To do so, we created colonies in which the queen was artificially inseminated with sperm from either one or ten drones. The colonies were established in early spring and their disease loads and strengths were measured in late summer. Of the 20 colonies studied, 80% contracted at least one brood pathogen and 75% contracted at least one adult parasite. We found significant differences between the two types of colonies for the prevalence of the brood disease chalkbrood and for the total prevalence of all brood diseases (chalkbrood, sacbrood, American foulbrood, and European foulbrood), with both variables lower for the colonies with higher genetic diversity. Our findings demonstrate that disease can be an important factor in the ecology of honey bee colonies living in nature, and they provide strong support for the parasite/pathogen hypothesis for the evolution of polyandry by social insect queens.