The sea trade has always played a significant role in both the business success of shipping companies and the welfare of the nations. The container storage yard is the geographical and operational centre of the container terminals in most seaports. As a result, it is very important and plays one of the major roles for the trade and transportation flows. One of the very latest developments in the operations relating the storage of the containers is the implementation of the automated rail mounted gantry crane system offering the very dense stacking of the units and lower labour costs. This publication was written with the purpose to investigate if the operational performance of the above mentioned seaport container terminals is influenced by the design of the storage systems and find out to what exactly extent this performance is affected by the framework conditions at the terminal. In addition, it is discussed the strategies applicable to the crane scheduling and stacking of the containers. The authors present a very detailed simulation model in order to compare the performance effects of some other storage designs as well as innovative planning strategies. This is a very useful and informative publication for people involved in storage and transportation of the shipping containers.