||This thesis deals with problems which importance increases proportionally to revival of the whole non-profit area in the Czech Republic during the past decade. The establishment of the democratic system gave a new stimulus to its new development. The non-profit organisations are entire part of the economics of the developed countries at present. Non-profit organisations fill the spaces where the so-called market failures happen. Their main task and aim is not to make a profit but to provide services when "invisible arm of the market" fails. The fact does not mean that they cannot reach a profit. A special emphasis is put on mission, which is the reason for creating the non-profit organisations, and the profit (incomes) is on the second place. These reasons are the main subject why the taxation of non-profit organisations has its specifics, which make the scope of this thesis.