Handling of biofuels may release dust particles containing high concentrations of Hazardous microorganisms, thus representing a potential occupational health problem. We analysed the microbial dustiness of baled straw (cultivated both conventionally and ecologically) and of wood chips from piles that had been stored outdoors for up to 11 months by using total spore counting, cultivation, and measuring of endotoxin and chemical markers of fungal biomass, lipopolysaccharide, and peptidoglycan. The bacterial dustiness of straw was much greater than of wood chips whereas the fungal dustiness did not differ much. In general, samples taken from the inner part of each biofuel material were dustier than samples taken from the surface, except for fungal and bacterial biomass in wood chips and total fungi and fungal biomass in ecological straw. A considerable increase of bacterial dustiness occurred during storage over summer. Dust from ecological straw contained considerably less of bacterial components than from conventional straw and, in addition, exhibited a less pronounced increase upon storage over summer. In summary, biofuels represent sustainable energy resources of growing economic importance but may at the same time pose significant health problems. We found that storage of biofuels outdoors over summer increased the microbiological dustiness and should therefore be avoided, and that ecological straw contained less of microbe-containing dust than conventional straw and should be preferred since it reduces the exposure to harmful microbiological agents.