The benchmark dose (BMD) approach is being increasingly used in the area of food risk assessment because it offers several advantages compared to the conventional no-observed-adverse-effect-level approach. The aim of this work was to check the applicability of the BMD approach on toxicity data available from pesticides, mycotoxins and natural toxins. Based on toxicological evaluations, the pivotal study was identified. Detailed data from the original study were retrieved and used for BMD modelling. Twenty-five studies used for BMD modelling were analysed with regard to study design: total number of animals, number of dose levels, and spacing between dose levels. The quality of the modelled endpoints was evaluated according to the following aspects: BMD/BMDL ratio, test for goodness of fit and BMD in the range of dose levels. If one of these aspects was not fulfilled, the BMD derived from this endpoint was considered to be uncertain to some extent and corresponding modelled data sets were examined. The present work demonstrates that the BMD approach is in principle applicable to pesticides, mycotoxins, and natural toxins. Although large differences relating to data availability and data quality were noticed, 69 of 82 modelled endpoints (84%) fulfilled the three quality aspects of BMD modelling.