A sequential extraction allowing the discrimination of water-soluble and non-soluble selenium fractions has been developed to evaluate the availability of selenium (Se) in an Se-enriched yeast candidate reference material. The fractionation of selenium-containing compounds in the extracts was achieved on preparative grade Superdex 75 and 200 columns. It showed that water-soluble selenium is present in several fractions with a large mass distribution. Low-molecular- (≤10 000) and high-molecular-mass selenocompounds (range 10 000–100 000) were considered separately for further experiments. The analytical approach for low-molecular-mass selenocompounds was based on anion-exchange HPLC with on-line inductively coupled plasma (ICP) MS for quantitative analysis. Selenocystine, selenomethionine, selenite and selenate were quantified in the fractions isolated in preparative chromatography. The study revealed the existence of various unidentified Se species in yeast material. The Se-containing proteins in the yeast material have been further separated and selenium quantified by the combination of gel electrophoresis and electrothermal vaporization–ICP-MS. This new approach allows the separation of the proteins with high resolution by sodium dodecylsulfate–polyacrylamide gel electrophoresis and the sensitive determination of selenium in the protein bands.