Handling of biofuels may release dust particles containing high concentrationsof Hazardous microorganisms, thus representing a potential occupational health problem. We analysed themicrobial dustiness of baled straw (cultivated both conventionally and ecologically) and of wood chipsfrom 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 didnot differ much. In general, samples taken from the inner part of each biofuel material were dustierthan samples taken from the surface, except for fungal and bacterial biomass in wood chips and totalfungi and fungal biomass in ecological straw. A considerable increase of bacterial dustiness occurredduring storage over summer. Dust from ecological straw contained considerably less of bacterial componentsthan from conventional straw and, in addition, exhibited a less pronounced increase upon storage oversummer. In summary, biofuels represent sustainable energy resources of growing economic importance butmay at the same time pose significant health problems. We found that storage of biofuels outdoors oversummer increased the microbiological dustiness and should therefore be avoided, and that ecological strawcontained less of microbe-containing dust than conventional straw and should be preferred since it reducesthe exposure to harmful microbiological agents.