We are trying to quantify all relevant costs connected with the railways operation in the Slovak and Czech Republic. We start with the direct costs of railway operation present in the accounting of the rail operator Cźech Railways, Railway Copany Slovakia and infrastructure manager, Railway Infrastructure Administration Czech Republic, The Railways of the Slovak Republic. Then we continue the analyses with the more hidden costs of railways present in the accounting of rail track operator, State Fund of Transport Infrastructure and directly in the state budget. We sort subsidies into two parts: direct and indirect railway's subsidies in the Slovak and Czech Republic. We are trying to evaluate the total costs of railway transport for public budgets and formulate recommodation for economic policy in the railway sector.