The present study deals with the impact of hydrocarbons on changes in the physical properties of the sediments of the Zdanice-Hustopece strata in the flysch sedimentary cover in the south-eastern part of the Czech Republic. The discussed changes are mainly concerned with contents of natural radioactive elements Th, U and K. The subjects of the study are rocks from deep boreholes collected down to the depth of 3.3 km. The boreholes are situated in an area of local hydrocarbon occurrences and are divided into two groups — with and without hydrocarbon indications. Physical properties of sandstones and claystones from the two groups are compared. It has been concluded that the distribution of U and K in the Zdanice-Hustopece Formation indicates shifts in contents of these elements which are undoubtedly due to the presence of hydrocarbons.