The European Structural and Investment Funds are an integral part of the Czech Republic, which helps both municipalities and cities, as well as business entities in individual regions. European Union funds are an important tool for implementing European economic and social cohesion. Using the funds are distributed funds intended to reduce economic and social disparities between the Member States and their regions. The aim of the article is to find out the situation between supported projects from the programming period 2014-2020 according to individual types of programs at the national and regional level (NUTS 3) in the Czech Republic. The author of this article focused on the comparison of the Operational Programs, area of intervention, collaboration, and total eligible expenditure allocated to the operation. Emphasis is then placed on a more detailed selection of the priority axis Protection and care for nature and landscape, which is part of the Operational Program Environment and the priority axis Improving public services and conditions for residents of the region, which is included in the Integrated Regional Operational Program. Within the given priority axes, the author of the paper also focused on regional comparisons at the NUTS 3 level in the Czech Republic.