The health status of the honey bee populations has attracted a great amount of interest in recent years. We investigated honey bee health in five natural protected areas in Italy from October 2009 to December 2010. Areas were selected to represent a wide range of bio‑geographical zones including alpine, continental, and Mediterranean. Within each of these natural protected areas, one apiary of 20 colonies near potential pollution sources (e.g., agricultural areas, industrial areas, or urban settlements) and another apiary of 20 colonies far from possible sources of pollutants have been placed. To monitor honey bee health, colony mortality was related to: honey bee pathologies, environment (Naturality Index, plant protection products and heavy metal exposure), and apiary management. Anthropogenic pollutants and pathogens did not have significant effects on colony mortality while environment and the poor colony management skills of the beekeepers did.