Special economic zones were formed to attract investment and encourage development of economic activity. Income generated by entities pursuing economic activity in special economic zones is exempted from income tax stipulated in zonal permit. It should be noted that zonal exemption is a form of limited state aid monitored by European and local administration bodies. Due to this fact taxpayer is obliged to control the consumed state aid. Additionally, zonal exemption requires separation of the zonal revenues and costs from the total amount of revenues and costs. The article presents problem with the settlement of state aid on account of the economic activity in special economic zone in the light of Regulation of the Council of Ministers regarding the methods of calculation of the value of state aid and the Treaty on the Functioning of the European Union (definition of the state aid). The main aim of this publication is thorough analysis of zonal loss and tax loss and their influence on the amount of state aid and the tax exemption. As a result, author defines main factors which are crucial for the proper calculation of the tax base for activity pursuing in special economic zones.