Food contaminants have many origins including soil, water and air. The latter environment may contain biological or non-biological particles that cause chronic respiratory disease and contaminate food exposed to it. Respiratory diseases rank fourth after cancer, diabetes and cardiovascular diseases worldwide in the list of priority non-communicable diseases that are the leading cause of death in the world. Among the most frequent microbiological pollutants, some moulds are responsible for respiratory diseases. Thus, man is exposed to this danger both in homes and in some of his activities. Some trades are the most exposed and also constitute cross-contamination frameworks for food. This is the case for millers and grain mills. The work presented here focused on particulate and fungal contamination of the atmosphere of cereal mills in the city of Cotonou. The fungal flora contaminating the atmosphere of the mills was assessed on direct samples by gravitational thrust and the particle size was estimated by suction on a pump equipped with a filter. The identification of fungal species is carried out morphologically and their metabolites by TLC. At the end of the work, after isolation of the different strains, the fungal flora of these mills was mainly composed of fungal particles (spores and fragments) of moulds of the genus Rhizopus nigricans, Mucor spp., Alternaria sp., Penicillium spp., Aspergillus niger, Aspergillus fumigatus and Aspergillus section Flavi. The isolated particulate air contaminants were of different sizes but mostly ultra fine. With an inspired average load of 1.15 to 47.55 mg/min. The working conditions of millers could favour the development of chronic respiratory diseases and even certain types of cancers for sensitive subjects. The investigation of the toxinogenic nature of the Aspergillus of the Flavi section in the mill atmosphere identified 10 aflatoxin type B and 19 aflatoxin type B and 19 aflatoxin B and G producing strains and only one non-aflatoxinogen. This high fungal load could also be the basis for contamination of the cereals that are deposited in its mills.