The paper focuses on taxation of non-residents from the European Union in the Czech Republic and their possible discrimination from the income tax point of view. It provides detailed comparative analyses of taxation of tax resident and tax non-resident workers (both employees and self-employed) in the Czech Republic. Thorough analysis discusses the issue of discrimination on all levels of taxation taking into consideration tax base, allowances, rates, tax credits as well as tax administration obligations. Unique overview of number of non-residents in the Czech Republic in 2004-2010 shows the importance of the topic. Since the social security contributions are inseparable part of obligatory payments, the paper discusses also their role in international taxation and possible discrimination issues briefly. Results of the analysis show that national tax legislation of the Czech Republic in the field of personal income tax is compliant with the relevant Court of Justice of the EU’s decisions. It also meets criteria of tax nondiscrimination principles of locational neutrality (fully) and competitive neutrality (partially).