Oats (Avena sativa L.) among the basic cereals are highly appreciated from the nutritive and the dietetic point of view. This beneficial effect of oat products is primary attributed to the soluble dietary fibre compound β-D-glucan, major polysaccharide constituent of cell walls of oats. Mature grains of naked oat genotypes dispose of higher content of β-D-glucan (Havrlentová and Kraic, 2006) and its value decreases in milled grain with time (Gajdošová et al., 2007). Locality and year influence its content, although it seems that the genotypes with black colour of the glumes account significantly lower standard deviation and variation coefficients in the content of β-D-glucan, what indicates markedly stable biosynthetic mechanism of studied metabolite (Čertík et al., unpublished data). Oat seed is also an important source of dietary fibre and its content can be influenced by both genotype and locality. The importance and exploitation of oats have an increasing style and therefore the monitoring of microsatellite polymorphism of Avena sativa DNA has his foundation. 20 pairs of microsatellite primers occurring in non-coding regions of DNA were tested. The best value of DI (0.938), the maximum value of PIC (0.938), and the minimum value of PI (0.000) was found in the microsatellite AM1. Generally, the oat DNA seems to be very conservative