The freedom of movement of individuals and the free circulation of goods in the European Community are fundamental components of the European construction. These freedoms have been endangered by the emergence of the new brand of international terrorism since 11 September 2001, which has jeopardised the safety of transportation all across the continent. To respond to this threat, the European Union has since been developing a vast range of legislative tools to secure its aviation and maritime transportation systems and to enable EU citizens to continue to enjoy their fundamental freedoms. This paper attempts to provide an overview of recent measures adopted by the European institutions to strengthen and co-ordinate air and maritime security in Member States. While describing the appraisable adoption of a wide ranged legislation, some of the main inadequacies emerge, such as concerns with fundamental rights of the individuals and the lack of efficient action in key sectors as critical infrastructures.