The paper presents the results of research focusing on the modelling the impact of the EU enlargement on agriculture of the Czech Republic and Slovakia. The research has been conducted under the AG-MEMOD of the 5th Framework Programme. The Czech Republic and Slovakia joined the European Union (EU) in May 2004 and became part of the single European agricultural market. The impacts of three scenarios (non-accession and two accession scenarios with SAPS and SPS introduction) are investigated. The paper concentrates mostly on pig and potato sectors. The Common Agricultural Policy (CAP) is expected to adversely affect these two sectors. This is expected to be the case especially in Slovakia. The main reason is that these sectors faced higher domestic prices and higher support level before accession, while accession will lead to a limited support and price decline. Also continued restructuring is an additional factor that will affect these sectors after accession.