This article presents the safety management issue in rail transport in the context of the principles defined in the European Union regulations, i.e., the Common Safety Methods (CSM) dedicated to risk assessment. It describes regulations applicable to the process of risk assessment process including risk analysis and evaluation. The most important challenges related to the application of risk assessment methods are also presented in the article. The regulations of the European Union do not precisely define the way in which risk assessment should be carried out in an organisation. Furthermore, the legislation only requires a risk assessment process to be carried out following a change to the railway system if such a change is assessed as a 'significant change'. This aspect remains problematic in the railway system, due to the considerable discretion left to the railway companies in their approach to conducting assessments of the significance of a change and the low percentage of so-called “significant changes”. As shown by some railway accidents and reports of the State Commission for Investigation of Railway Accidents, omissions in the process of risk assessment and inconsistency of approach of various undertakings to analogous situations may lead to an uncontrolled increase in the level of risk in railway transport.