Global population increases, coupled with intensive animal and livestock production practices, have resulted in the generation, accumulation, and disposal of large amounts of wastes around the world. Aerosolization of microbial pathogens, endotoxins, odors, and dust particles is an inevitable consequence of the generation and handling of waste material. Bioaerosols can be a source of microbial pathogens, endotoxins, and other allergens. Given the close proximity of population centers to concentrated animal-rearing operations and municipal treatment facilities in many parts of the world, there is concern regarding the occupational and public health impacts associated with the exposure to bioaerosols from municipal and animal wastes. Major advances have been made in our understanding of bioaerosol characteristics, identifying the hazards, and identifying possible human and animal health links with aerosolized pathogens and allergens. However, significant knowledge and technology gaps still exist. These include a lack of clear understanding of the fate and transport of bioaerosols, especially within the open environment, an inability to accurately predict the health risks associated with bioaerosolized pathogens, and a lack of standardized bioaerosol sampling protocols, and efficient samplers. This review synthesizes the information related to bioaerosols and addresses the contemporary issues associated with bioaerosols from municipal and animal wastes, with a focus on pathogens.