The range of direct and indirect effects of railway transport on animals, plants, ecological processes and the actual ecosystems vary considerably. Railway transport operations and infrastructure building lead to environmental pollution, loss or conversion of habitats, landscape fragmentation and, last but not least, to animal mortality caused by collisions with passing trains. The impact of railways is determined by the nature of railway infrastructure, which is not as significant in the Czech Republic as road infrastructure, yet it is one of the densest in Europe. An important feature is relatively low electrification (about 33% of the lines) and the length of multi-track lines (about 20%). In the coming years, we can expect massive investments in revitalization, optimization and modernization of the railways in the Czech Republic, and eventually their electrification. To connect the crucial trans-European lines and all regions it will be necessary to complete the basic network of high-speed railways. Based on these facts we can say that the significance of railway ecology in the Czech Republic will grow with the amount of investment activities implemented in the railway network. In the past, similar development took place with road infrastructure, and therefore there is an opportunity to learn from it. To mitigate the direct effects of railways on wildlife, on the basis of previous experience in the Czech Republic we recommend working primarily with management measures. These are both in terms of wildlife management and the management of habitats in the area of transport infrastructure.