BACKGROUND: During the pretreatment of lignocellulosic materials, molecules such as carboxylic acids, furan derivatives and phenolic compounds, which inhibit the growth and ethanol fermentation by bacteria, fungi and yeasts, are produced. The present work determines the tolerance levels of the C5, C6 fermenting fungus Fusarium oxysporum, towards individual model inhibitory compounds on aerobic growth, on lignocellulolytic activities and on fermentative performance. RESULTS: During the growth stage, maximum biomass production was more affected than the specific growth rate by the presence of inhibitors. The presence of high concentrations of inhibitors resulted, in most cases, in prolongation of the lag phase. The fermentative performance of F. oxysporum was significantly inhibited by carboxylic acids, while the lignocellulolytic activities were affected to a lesser extent. CONCLUSION: The toxicity tolerance of F. oxysporum was high enough for aerobic growth in the presence of significant concentrations of inhibitors, which in most cases were higher than those generated from various treatments of lignocellulosic materials, while its fermentative performance was relatively more affected by the presence of inhibitors. The decrease of ethanol production in the presence of weak organic acids could be the main obstacle to the application of F. oxysporum in large-scale bioconversion processes of hydrolysates containing inhibitors. (C) 2010 Society of Chemical Industry