In this work, microscopic X-ray absorption near-edge structure spectroscopy (mu-XANES) and confocal microscopic X-ray fluorescence analysis (mu-XRF) were used for the in vivo determination of the distribution of total selenium and for the local speciation of selenium in roots and leaves of onion. Selected Allium cepa L. plants were grown hydroponically in a standard medium containing inorganic selenium compounds (selenite or selenate). The measurements were performed in vivo, that is, on living plants without the need for any form of sampling or sample pretreatment and without the necessity for cutting plant tissues into pieces. Distinct energy differences of the XANES spectra of various selenium reference compounds having different oxidation states allow adjusting the excitation energies used for mu-XRF mapping in such a manner that the distribution of selenium in various oxidation states is obtained with a spatial resolution of a few tens of micrometers within the virtual cross section of the onion tissues. We find that the ratio of inorganic to amino acid selenium compounds differs in various subparts of the plant. Detailed in vivo investigation of the distribution of various selenium species in virtual cross sections of root tips and green leaf shows that the selenium transport takes place via different mechanisms, depending on the nature of the selenium compounds originally taken up.