A sequential extraction procedure was developed for the fractionation of different classes of selenium species present in garlic. The consecutive steps included leaching with water, extraction of cell-wall bound species after lysis with a mixture of cellulase, chitinase and β-glucanase completed by a proteolytic attack, extraction with HCl to liberate the residual organic bound species and finally, extractions with sulfite solution and CS2 to complete the mass balance by the recovery of Se0 and Se2-, respectively. Selenium speciation in the aqueous fractions was probed by anion-exchange and ion-pairing reversed-phase HPLC-ICP MS after purification by preparative size-exclusion LC. It was found to be strongly affected by the sample redox conditions. The peak identity was matched with a mixture of 9 compounds expected to be present in allium plants; electrospray QTOF MS turned out to be unsuccessful. Selenite, selenate and selenomethionine were the dominating species present.