The work analyses the current status of harmonization of valued added tax (VAT) and excise tax on mineral oils and wine in Slovakia. In particular, attention is paid to an impact of legislation changes to these taxes on agricultural companies. Generally, it can be conluded that the harmonization process concerning the above taxes has been finished, and the remaining problematic questions, which are mainly associated with a change in the existing tax regimes, can only be harmonized after the accession of Slovakia to the European Union.