The cadmium hyperaccumulator Thlaspi praecox Wulfen (Brassicaceae) can accumulate unusually high amounts of Cd (>1,000 μg g −1 dry weight) in its seeds without drastically affecting seed viability. As embryonic tissues are the most sensitive to Cd toxicity, the aim of this study was to investigate the Cd coordination and ligand environment in seeds of field collected T. praecox using extended X-ray absorption fine structure (EXAFS), and to compare the Cd ligand environment to that in the vegetative tissues of the plant. In intact seeds and isolated embryos, almost two thirds of the Cd ligands were thiol groups (Cd-S-C-).In addition, there was coordination to phosphate groups via bridging oxygens (Cd-O-P-), as for phytate, although this ligand was not observed in the vegetative organs and tissues. In roots and shoots up to 80% of the Cd ligands were oxygen ligands that are provided by the cell walls and by organic acids stored in vacuoles. In leaf epidermis only a slightly higher percentage of oxygen ligands was detected, as compared to the mesophyll, making vacuolar compartmentation and binding to the cell walls the main detoxification mechanisms in both of these leaf tissues.