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The theory and policy of taxation of financial services has significantly changed in recent years, due primarily to the financial crisis. Theory requires the coordination of the financial sector taxation and regulation, and analyses the effectiveness of introducing special taxes. This newly opens up the issues of value added tax and the existing exemption of financial services from it. Markets are moreover distorted by government subsidies for different financial products. The authors´ primary aim is the critical review of the literature and derivation of the recommendations for the taxation of financial services in the Czech Republic. Financial services need to be temporarily subjected to the financial activities tax until these services are duly subject to the value added tax in the EU. A major reform of value added tax, such as the transition to income type of this tax, would ease the solution of the existing problems.