When examining the proper functioning of the principle of the separation of powers not only the institutional design of state institutions and their formal powers shall be taken into consideration. Legal institutions with primary functions not related to the system of the separation of powers can also affect the sphere of action of state powers, especially the majoritarian power. Tools of minority direct democracy (citizens’ initiatives, referenda initiated by a minority), internal limits of the legislative power (open debate, supermajority requirements), as well as the application of certain doctrines developed in constitutional interpretation and methods of reasoning (informal constitutional amendments, proportionality), can function as ‘invisible checks and balances’. Taking into consideration this ‘invisible side’ of the system of the separation of powers supports the more precise analysis of the state of the separated powers in a given country.