Terrorism presents a greater threat to national and transnational security today than it has presented at any time in history. Authors outline the most important issues regarding investigating contemporary terrorism. They argue that smart organization of investigation process in crisis situations caused by terrorism is critical for the effective implementation of investigation plan. The plan reflects all the elements of the case, defines investigation team and serves as a guide for resources use (human, technical, information). If we observe the investigation as a process, a case does not end by solving crisis because managers must bear in mind the long-term aspects of everything carried out during the investigation. An adequate organization enables investigation to be analyzed in objective way with minimizing possibilities for errors. It is important that managers value the ideas based on their content and not the origin and the effect it has on the team.