The aim of this thesis is to reduce the number of negative audit findings, by improving the quality of project management Czech Social Security Administration (hereinafter the "CSSA") in the form of draft amendments to the project management methodology and system changes within the organization. The proposals will be based on the evaluation of existing project management methodology applied in the implementation of projects financed from EU Structural Funds in the programming period 2007 - 2013 with an emphasis on the possibilities of the proposed changes in the period 2014-2020. The theoretical part defines basic terms as Czech Social Security Administration, project management methodology PRINCE2, European structural and investment funds, programming period 2014-2020 and operational programs of the Czech Republic. The practical part begins with a brief introduction of project management directive Czech Social Security Administration no. 16/2013 and projects implemented by this organization in the programming period 2007-2013. Following analysis of the applicable project management methodology and the CSSA internal processes along with project documentation and structured interviews with selected respondents from the environment of the CSSA. The conclusion is based on analyzes of identified shortcomings analyzed environment and also proposes measures for their elimination.