Three sample preparation methods--proteolysis to determine the initial species distribution, and an in vitro gastric and gastrointestinal digestion to assess the bioavailability of selenium--were applied to extract the selenium from selenized green onion and chive samples. Ion exchange chromatography was coupled to a high-performance liquid chromatography-ICP-MS system to analyze the selenium species of Allium samples. The difference in the selenium accumulation capability of green onions and chives was significant. Chive accumulated a one order of magnitude higher amount of selenium than did green onion. After proteolysis of both types of Allium plants, high amounts of organic selenium species such as MeSeCys, SeCys2 and SeMet became accessible. In the case of Se(VI)-enrichment, selenate was the main species in the proteolytic extract. After simulating the human digestion, the organic species were just slightly bioavailable compared with the results from proteolysis. The inorganic selenium content of the selenized samples increased significantly and SeOMet could be detected from the extracts. As an effect of the significant pH change between the gastric and the intestinal tracts, two oxidation processes took place: selenite oxidized to selenate, while SeMet oxidized to SeOMet.