The paper aims to define limitations for implementation of tax certainty principle in the process of designing modern tax systems. In the era of globalisation and expansion of cross-border business, taxpayers are facing with problem of tax compliance in more than one jurisdiction, and tax administrations with problem of determination of proper tax treatment. Tax uncertainty seriously affects liquidity, business and business strategies of taxpayers, and, at the macro level, investment, trade and revenue collection. The research in the paper has shown that its application in modern states is jeopardised, since tax systems have become more complex, not only in the sphere of legislation, but also in the field of implementation of tax laws. It has been concluded that modern financial flows request a redefinition of principle of tax certainty and an achievement of the balance between tax certainty and desirable degree of tax uncertainty, which is needed for implementation of tax reforms and greater flexibility of tax policy, as strong instrument in the time of economic crisis.