Microcystins (MCs) are cyclic heptapeptides and protein phosphatase inhibitors produced by many species of cyanobacteria. MCs have been shown to cause adverse effects on animals as well as plants and therefore methods are needed for analysing MCs in different matrices. We assessed the effects of MC exposure on broccoli (Brassica oleracea var. italica) and mustard (Sinapis alba) by watering the seedlings with water containing 0, 1 or 10 μg MCs L-1 (concentrations typically found in natural waters). Morphological characteristics, chlorophyll concentrations and chlorophyll fluorescence were investigated, but the only distinct difference compared to control plants was a slight (<10%) growth inhibition seen in broccoli. Afterwards the MC concentration of selected plant samples was quantitated using liquid chromatography-mass spectrometry. Among the four MC variants present in the exposure mixture, only MC-LR was clearly detectable, and the toxin was found only in the roots of broccoli and mustard. The detected MC-LR concentrations ranged from 0.9 to 2.6 ng (g fresh weight)-1.