Investigations on airborne fungi in a poultry house, a swinery, a feed preparing and storing house, a grain mill, a wooden panel producing factory, and organic waste recycling facilities have been carried out in Lithuania. Low concentrations of fungal spores were detected in the wooden panel producing factory, the swinery, the feed preparing and storing house, and the poultry house; moderate concentrations were found in the organic waste recycling facilities; high concentrations were revealed at the grain mill. Species of Aspergillus oryzae, A. nidulans, P. expansum, Penicillium olivinoviride, P. claviforme and Botryotrichum longibrachiatum prevailed in the poultry farm; Geotrichum candidum, Cladosporium cladosporioides, C. herbarum, Penicillium viridicatum and P. fellutanum dominated in the swinery. Fungi of Penicillium viridicatum, P. expansum, Staphylotrichum coccosporum and Aspergillus oryzae prevailed in the feed preparing and storing house at the swinery. Cladosporium cladosporioides, C. herbarum, Penicillium viridicatum and Geotrichum candidum prevailed in the grain mill. Fungi ascribed as Paecilomyces puntonii, Rhizopus nodosus and R. stolonifer dominated in the wooden panel producing factory. Species of Aspergillus raperi, P. paxilli, P. oxalicum, and Cladosporium herbarum prevailed at the organic waste recycling facilities. According to published data, the majority of the identified fungal species are characterized as allergenic and an exposure to their spores may provoke adverse health effects (such as allergic rhinitis, bronchial asthma or extrinsic allergic alveolitis) in susceptible individuals.