Grain storage conditions affect its quality. In Lithuania, different types of farms have various harvesting, processing and storing conditions. Grain samples were tested from agricultural granaries of 3 different types with different grain storage conditions in Lithuania. During March-April in 2001 the investigation on mycological and mycotoxicological state of stored grain from different types of agricultural granaries were performed. Wheat (Triticum aestivum L.) samples (n = 33) were tested from small, medium and large granaries. Barley (Hordeum distichon L.) (n = 22) was tested from small and medium granaries. Considering this issue, 31 species of micromycetes ascribed to 8 genera were isolated and identified. The results obtained indicate that highest levels of micromycetes contamination are found in small granaries with good storing and drying equipment. Micromycetes of some species belonging to the Penicillium Link, Aspergillus Mich. Ex Fr., Fusarium Link, and other genera, are able to produce secondary metabolites - mycotoxins of various compositions that are toxic to plants, animals, and humans. The levels of mycotoxins zearalenone and ochratoxin A were established. The highest concentration of zearalenone and ochratoxin A were found in grains from small farm granaries.