The livestock sector plays an essential role in food production and food security. The investigation carried out on the Institute of Animal Science of Lithuanian Veterinary Academy in 2003-2004 at the Department of Animal Hygiene and Ecology. The goals of this study were twofold: 1) to estimate microbiological risk on the poultry farms, and 2) to determine species diversity of molds fungi in the indoor environment of the poultry farms in the northen region of Lithuania. This study has found that levels of moulds contamination in poultry farms vary among the different keeping coditions: for laying hens - moulds count in the air was 0.43 +/- 0.18 thous. CFU m(-3) (in the cage system) and 0.83 +/- 0.13 thous. CFU m(-3) (in the litter floor system); for turkey - 3.82 +/- 0.211 thous. CFU m(-3) (keeping on straw) and 14.97 +/- 3.25 thous. CFU m(-3) (keeping off peat). Values differ significantly At P<0.05. The results showed that mould species of genera Aspergillus, Fusarium, Mucor, Penicillium were most frequent in the communities of fungi in all substrates (litter, indoor air, water and feed) of poultry farms. The litter and air samples are contaminated with moulds at a higher level. Micromycetes of 39 species were identified from different substrates (litter, indoor air, water and feed) in poultry farms indoor environment. Aspergillus is the most numerous genus of the dominant group (38.5-49.3%). Micromycetes of 39 species were identified from different substrates (litter, indoor air, water and feed) on poultry farms (geese, turkey, laying hens, broilers, ducks) in northen region of Lithuania. The litter and air samples were contaminated with moulds at a higher level. The level of moulds contamination in poultry farms vary among the different poultry keeping coditions.