Income taxation is of great importance for small and medium enterprises (SME) because of direct influence on their funds. Changes in these taxes in last few years has mostly a positive effect on SME activity and development. Such examples are tax credit, simplified advances, deduction from income the expenditures for new technology, high amortization rate, possibility of use the linear rate of 19%. Positive aspects had also changes in lump sum, especially broadening of the taxation range. However, income taxes has a negative influence on SME due to instability, various interpretations, complexity, luck of precision, difficulties in planning. Elimination of them will improve the SME situation, will increase the certainty of the taxes.