A method to determine the selenium distribution in milk whey fractions was developed. After milk whey preconcentration by ultrafiltration, selenium in the protein fractions was separated by size exclusion chromatography (SEC) and determined by electrothermal atomic absorption spectroscopy (ETAAS) using a sampling procedure based on fraction collection, fraction preconcentration by ultrafiltration and introduction into the furnace after digestion, hydride generation and hydride preconcentration. The digestion and reduction conditions of the milk whey fractions obtained by SEC were studied. The hydride generation parameters and preconcentration into an iridium coated graphite tube using ETAAS with a Zeeman background correction were optimised. The method was applied to six infant formula milks and selenium was found in three fractions of cow-based infant formulas: 40 kDa, >160 kDa and mostly in the <10 kDa fraction.