Investigations are described to extract Se-species from a bacterial sample. The five extraction methods investigated were: hot water, protease, lysozyme, lysozyme-protease, and HCl hydrolysis. The extraction efficiency was determined by comparing the total amounts of selenium in the sample after pressure digestion with the amounts extracted by the different methods described. Efficiencies were found to be only 1% (hot water), ca. 8% (protease, HCl hydrolysis) or ca. 12% (lysozyme, lysozyme-protease). The Se-peak patterns were compared after investigating the extracts with strong anion exchange chromatography–inductively coupled plasma mass spectrometry (SAX–ICP–MS). Most promising were the lysozyme-assisted procedures, which showed the highest diversity of species. Here, in the protease-lysozyme approach, the protease seemed to break down species that had been extracted by lysozyme from the bacterial wall (murein sacculus). The other approaches seemed not to extract many species. Hot water extraction was completely unsuitable, extracting only low amounts of a single, unknown species.