The object of the study was to investigate the influence fertilization on the β-glucan content of the common oats varieties (Vendelin, Zvolen) and the naked oats varieties (Detvan, Avenuda). The trial was established in the years 2007 and 2008 in the potato growing area in the centre of Slovakia in Vígľaš-Pstruša. The field treatments were realized in natural conditions without irrigation with four variants of fertilization. Nitrogen fertilization was applied before sowing and foliar application of selenium together with nitrogen was done in the growth phase at the end of stooling (BBCH 29). The amount of β-glucan in the samples was determined by using the β-glucan assay kit (Megazyme, Ldt. Ireland). The total average of β-glucan content in the experiment was 4.08 %. The naked oats varieties reached higher content of β-glucan, when we compare it with the common oats. The variety Avenuda reached highest of β-glucan content (5.20 %). The nitrogen fertilization together with selenium fertilization statistically significantly increased the content of this polysaccharides. The influence of a particular year was statistically significant in β-glucan content.