Providing an efficient, safe and secure transportation service is a core factor for European growth, collaboration and employment. As such, this has been identified as a priority in the Europe 2020 strategy. Land transportation has two main challenges concerning security: avoiding interrupts of transport itself in order to assure the flow of freight and passengers and avoiding those transportation systems themselves become a mean for attacks. The European project CARONTE (Creating an Agenda for Research on Transportation security) intends to establish a future research agenda for security in land transport, which focuses on the relevant security gaps caused by emerging risks. Considering the current state of the art and existing research projects, CARONTE covers all threats, including cyber-crime, and security aspects for all land transportation modes, with respect to fundamental human rights and privacy. Accordingly, this paper provides an overview on existing and emerging risks, in terms of security, facing the rail mode as well as the potential measures, based on the risk assessment methodology adopted in the project. This work explains how, from the project point of view, the rising of new cyber-risks and the fast evolution of threats led by technological progress in the rail industry constitute the main challenges of the European rail security nowadays.