The era of Marine Autonomous Surface Ships (MASS) has already begun, claiming, among others, the enhancement of both the, maritime safety as well as the protection of the marine environment. Systems engineering is a generic methodical approach that provides, the means for the management of complexity in the systems and the analysis of their safety. MASS are complex systems, therefore, systems engineering along with the relevant theory and methods may assist to the safety analysis of MASS and provide a solid basis, for realistic and exploitable results. This paper is the starting point of this research, that aims at the development of a framework and, the application of a specific methodology which will analyse the safety of MASS, for the various levels of autonomy, taking also into, account the role of the human within the system (i.e. human in or on the loop), to clearly identify the roles and tasks of human within, the MASS complex system and to enhance the overall safety.