The EU Cohesion Policy requires the interaction of the public, private and non-profit sectors in policy making. The Czech Republic presents an ideal case study for identifying the major obstacles to the successful implementation of this approach since Czech citizens evaluate Non-governmental organizations (NGOs) in their country as having less capacity to influence policies at the lowest level than NGOs in any other EU member state. The goal of the study is to identify and explain the determinants of success and failure regarding NGOs’ participation in designing public programmes. The methodology includes a combination of in-depth interviews with NGO representatives and public servants, a review of official documents, a focus group, and a stakeholders’ review of the study’s conclusions. The main obstacles to the implementation of the partnership principle are the following: NGOs’ insufficient capacities and responsibilities; fluctuations in the participation of public servants and NGO representatives; dependence of partnership on personal contacts; NGOs’ late entry and the non-consultative, informative character of the partnership.