Selenium is an essential element for human health. It has been recognized as an antioxidant and chemopreventive agent in cancer. Selenium is known to develop its biological activity via selenocysteine residue in the catalytically active centre of selenoproteins. The main source of selenium in human beings is the diet. However, in several regions of the world the content of selenium in diet has been estimated insufficient for a correct expression of the proteins. The beneficial effects of selenium on human health are strongly dependent on its chemical form and concentration. This review critically evaluated the state-of-the art of selenium speciation in biological matrices mainly focused in nutritional and food products. Besides the number of publications related to selenium speciation, isolation and accurate characterization and quantification of selenium species is still a challenge. Hyphenated techniques based on coupling chromatography separation with inductively coupled plasma spectrometry (ICP-MS) and its combination with molecular mass spectrometry (ESI-MS, ESI-MS-MS and MALDI-TOF) and isotopic dilution allow identification, quantification and structural characterization of selenium species. Particular attention is paid in the development of Se-enriched food and nutritional products and how the application of the techniques mentioned above is mandatory to get reliable results on selenium metabolisms in these particular matrices.