The thesis is dealing with development and evaluation of the Cross-Border Cooperation within the EU, as a part of the EU Cohesion policy, with Focus on the Czech Republic. The aim of the thesis is to evaluate the cross-border cooperation programmes in the Czech Republic from the applicants' and selected implementation structure subjects' point of view. These selected subjects are the Ministry for Regional Development of the CR, the Centre for Regional Development of the CR and administrative regions of the CR. The first part of the thesis refers to the history and development of the Cross-Border Cooperation within the EU and the CR and to the reasons which led to its establishment. The last part is focused on the description and the evaluation of applicants' and selected implementation structure subjects' experiences with cross-border cooperation programmes and their perception of the Cross-Border Cooperation in the CR. As a method for the evaluation of the cross-border cooperation programmes in the CR were used the following procedures: an analysis of the available publications and internet sources, interview with representatives of the Ministry for Regional Development of the CR and the Centre for Regional Development of the CR, and an inquiry via questionnaire among the administrative regions of the CR.