The article is concerned with the issue of eligibility of the value added tax, namely a possibility to have the VAT, paid by beneficiaries of the measures co-financed from the Programme for the Development of Rural Areas for 2007–2013, returned from the European Funds. The measures in question are those where the self-government of a region performs the tasks of the managing authority (as an implementing authority). Once VAT is excluded from eligible expenditures, the share of beneficiaries’ own funds increases significantly. The author discusses doubts concerning the eligibility of the tax paid by state authority bodies, especially self-governments, presenting various interpretations in the field. He also focuses on eligibility of the value added tax incurred by those entities that are exempt from this tax, which in his opinion is incorrect.