This article is devoted to the analysis of the establishment of the professional recognition systems in the European Union agreements with third countries. The issue of mutual recognition of professional qualifications is one of the key elements of the European Union economic integration with third countries. France-Quebec Agreement on Mutual Recognition of Qualifications is the first initiative between the European Union member state and a Canadian province. The agreement supports efforts aimed at negotiating an economic partnership between the European Union and Canada. The agreement applies to all regulated professions and trades in France and Québec, and is based on the recognition of qualifications. It sets frame for signing first Mutual recognition of professional qualifications agreements pertaining to some thirty trades and professions, and for the other regulated professions. The Canada-European Union Comprehensive Economic and Trade Agreement arrangements for the mutual recognition of qualifications grew out of the Franco - Québecois Agreement. The agreement provides a framework to facilitate the mutual recognition of qualifications in regulated professions such as architects, accountants and engineers. The relevant professional organizations in the European Union and Canada now have a framework that sets out the conditions for the negotiation of mutual recognition agreements for their respective professions. The agreement sets mechanism for professional recognition systems and procedure of its formation. It is an example of European Union cooperation with third countries and a new way of cooperation in the scope of mutual recognition. The mechanism of the European Union cooperation with third countries within the mutual recognition scope can be used by other integrational associations in particular by the Eurasian Economic Union.