The present article analyses the development and impact of the container security initiatives on maritime supply chains. Security issues concerning container liner shipping require complex approach and application of integrated IT systems on national and international levels. During the last two decades various initiatives have been applied to ensure for higher level of security of container transportation. The background and aim of these initiatives are studied in detail and their effect is evaluated. The results show that container transportation still has vulnerable nodes and the application scope of security initiatives is to be widened despite the high costs.