BACKGROUND: Three matrices - corn (maize) meal, distiller's dried grains with solubles (DDGS) and condensed distiller's solubles (CDS) - were sampled in sequence from a continuous dry-milling process plant for the determination of mass balance of deoxynivalenol (DON). Four commercially available enzyme-linked immunosorbent assay (ELISA) kits were evaluated for their ability to measure the presence of DON. Liquid chromatography/tandem mass spectrometry (LC/MS/MS) was used as standard method to detect DON and other Fusarium toxins. Results: The concentrations of DON in DDGS and especially CDS were over estimated or under estimated by ELISA. However, for both matrices, all ELISA methods were not significantly different in their mean results from the LC/MS/MS standard, although the variability in results was much higher. DON concentrations in the CDS and the final DDGS co-product were significantly higher (P ≤ 0.01) than in the starting material (corn grain). Toxin concentration increased by a factor of 3 on a dry weight basis in DDGS compared with the starting corn and by a factor of 4 in CDS. Mean concentration of DON in CDS was four times higher (7.11 mg kg-1) than in corn grains (1.80 mg kg-1) and 1.4 times higher than in DDGS (5.24 mg kg-1). Mass balance calculations showed that CDS was the main source of contamination of DON, comprising ca 70% of the toxin found in the final product (DDGS). Most DON (87%) was accounted for by this analysis. CONCLUSION: Concentrations in the grain corn entering ethanol plants should be close to the dietary values recommended for swine in Canada and the USA for DON (1 mg kg-1). Small amounts of acetyldeoxynivalenol and DON glucoside were also found in the three matrices along with a small amount of zearalenone. Unlike the situation for DON, the DON glucoside was not concentrated into DDGS and CDS, indicating that it was hydrolysed during the fermentation process. © 2009 Society of Chemical Industry.