The objective of the study was determination of the level and species composition of filamentous fungi and the concentration of mycotoxins in rape grain and dust produced during the threshing – from the aspect of potential health risk for private farmers. The study materials were samples of rape grain and dust taken during threshing on private farms. The concentration of filamentous fungi in the samples of rape grain and dust was determined by the method of patch testing with serial dilutions, while the concentration of mycotoxins – with the use of thin layer chromatography (TLC), and high performance thin layer chromatography method (HPTLC). Species composition of filamentous fungi was determined in the grain and dust of rape. In the samples of rape grain and dust taken during threshing the presence of many species of filamentous fungi was observed, known as etiologic factors of allergic, immunotoxic and mycotoxic respiratory diseases. During threshing, the rape dust concentration of filamentous fungi was high – 5.5 x 108 cfu/g, and constituted a potential health risk factor for farmers engaged in rape threshing. In rape grain and dust the presence of ochratoxin A was also noted, known as an etiologic factor of Balkan endemic nephropathy – a chronic renal disease. The study showed that farmers working in the environment contaminated with organic dust produced during rape threshing are exposed to inhalation of dust polluted with many species of filamentous fungi, which creates the risk of occurrence of allergic, immunotoxic and mycotoxic diseases of the respiratory system.