This paper concerns container shipping transportation viewed as an interdependent security system. The methodological background is the use of game-theory in the investigation of how interdependence affects individual choices about security expenditures in so-called interdependent systems (IDS problems). Any agent’s incentive to adopt security measures depends on the actions of others because of the negative externalities created among them. In this context, we examine security questions in container transportation and more specifically we focus on investments in container checking systems at ports, considering the currently much debated 100% scanning requirement of containers destined to USA. It is obvious, that in such analysis there is a demand to balance the cost of investing in (installing) and operating such a system and the reduction in the risk of a potential damage from a “dangerous” container from a security point of view. A transferred “dangerous container”, which may pass through another agent / port (screening point), introduces an additional dimension of risk. Useful suggestions are reached from such a treatment of the subject and policy dimensions emerge, such as the potential need for coordinating mechanisms among ports.