This paper aims to determine the effects of the transition on mutual trade between the countries of the former Yugoslavia. The research will be based on a qualitative and descriptive analysis of representative databases of the six countries mentioned for the time period after the disintegration of the SFRY. Economic reforms and the trade liberalisation process started even within the SFRY, but the reforms did not yield the desired results. After the disintegration of the SFRY, all countries independently defined the transition process and chose the path of European integration. In the first phase of the transition, all countries experienced recession and hyperinflation and a high foreign trade deficit due to trade liberalisation. The second phase was characterised by regulatory reform and institution building, but this process did not proceed at the same speed in all countries. After 2000, Slovenia was the only one with a higher export level as a percentage of GDP compared to imports (68.2%), and the other countries lagged significantly behind. When Slovenia and Croatia became EU members, they increased their foreign trade exchange with the EU. Other countries of the former Yugoslavia developed their mutual trade, primarily due to the CEFTA Agreement. By signing the agreement, all countries achieved export growth as a percentage of GDP, and the highest values of this indicator were recorded in North Macedonia (49.6%) and Serbia (40.8%). Within the CEFTA group, Serbia is the largest exporter and importer by value (its most important partner is Bosnia and Herzegovina). If we consider all the countries of the former SFRY, the largest exporter and importer is Slovenia, and its largest foreign trade partner is Croatia.