The explosive growth in the freight volumes has put a lot of pressure on seaport authorities to find better ways of doing daily operations in order to improve the performance and to cope with avalanches of containers processing at container terminals. Advanced technologies, and in particular automated guided vehicle systems (AGVS), have been recently proposed as possible candidates for improving the terminal’s efficiency not only due to their abilities of significantly improving the performance but also to the repetitive nature of operations in container terminals. The deployment of AGVS may not be as effective as expected if the container terminal suffers from a poor layout. In this paper, simulation models are developed and used to demonstrate the impact of automation and terminal layout on terminal performance. In particular, two terminals with different but commonly used yard configurations are considered for automation using AGVS. A multi attribute decision making (MADM) method is used to assess the performance of the two terminals and determine the optimal number of deployed automated guided vehicles (AGVs) in each terminal. The simulation results demonstrate that substantial performance can be gained using AGVS. Furthermore, the yard layout has an effect on the number of AGVs used and on performance.