Since 2006, beekeepers around the world have reported unusually high rates of honeybee colony loss. In the last two years, attention has turned to neonicotinoids as a potential factor in honeybee disease and mortality. While fatal at high doses, neonicotinoids are primarily used as seed treatments, and researchers debate whether honeybees are regularly exposed to these pesticides at sufficient doses to do harm. We combine unique geocoded data on apiary pollen samples and pest loads across 40 US states over the past 4 years with crop data to ask where and when we observe evidence of neonicotinoid exposure in the hive, and what effect that exposure has on honey bee health. We find that neonicotinoids are largely found in hives near neonicotinoid-treated crops during planting, and that colonies with neonicotinoid contamination have higher levels of Nosema, a virus associated with colony loss. We find no evidence of an effect of neonicotinoids on Varroa mites.