The studies on the characterisation of glucosinolates (GLs) and their breakdown products in Brassicaceae species focus mainly on the edible parts. However, other products, e.g., dietary supplements, may be produced also from non-edible parts such as roots or early forms of growth: seeds or sprouts. Biological activity of these products depends on quantitative and qualitative GL composition, but is also strictly determined by GL conversion rate to chemopreventive isothiocyanates (ITC) and indoles. The aim of this study was to evaluate the conversion rate of GLs to ITC and indoles for various plant parts of chosen Brassica species in relation to their biological activity. For this purpose, the composition of GLs and their degradation products was determined as well as activity of myrosinase. Toxicological part of studies involved: MTT assay, restriction analysis, comet assay and Ames test. The composition of GLs and conversion rate to ITC and indoles was found to differ significantly between Brassica species and individual parts of the plant. The highest efficiency of conversion was observed for edible parts of plants: more than 70%, while in sprouts, it reached less than 1%, though myrosinase activity did not differ. The conversion rate directly affected biological activity of plant material. Higher concentration of ITC/indoles in the sample led to the increase of cytotoxicity. Majority of tested samples were able to induce covalent DNA modification in cell-free system. It was also confirmed that the presence of indolic GLs and products of their degradation stimulated mutagenicity, but did not lead to DNA fragmentation in cultured cells.