Concentrations of fungal metabolites were measured in 32 wheat grain samples from north-eastern Poland in 2003. The samples originated from fields cultivated conventionally (but varying in chemical protection level) or cultivated organically. Concentrations of Fusarium toxins (HT-2, DON, 3-AcDON, NIV), trichodiene, microbial biomass indicators (fungal ergosterol and general adenosine 5'-triphosphate (ATP)) and seed vigour were assessed. A large variation between samples was observed, depending on their origin. Seed from organic farms contained similar amounts of Fusarium toxins but more ergosterol and ATP than conventionally grown and chemically protected seed. The highest levels of toxins and ergosterol were detected in samples from conventional cultivation lacking chemical protection. Intensive agronomic practices (including complete chemical protection) significantly lowered the levels of ergosterol, ATP and trichodiene, as compared with other cultivation systems.