The fluctuation of fuel price levels along with the continuous endeavour of the shipping industry for economic growth has led the shipbuilding industry to explore new designs for various types of ships. In addition, the introduction of new regulations by the International Maritime Organisation frequently triggers changes in the ship design process. In this respect, proper use of computer-aided ship design systems extends the design space, while generating competitive solutions in short lead time. This paper focuses on multi-objective optimisation of the design of containerships. The developed methodology is implemented on CAESES® software and is demonstrated by the conceptual design and optimisation of a 6,500 TEU containership. The methodology includes a parametric model of the ship’s external and internal geometry and the development and calculation of all required properties for compliance with the design constraints and verification of the key performance indicators. The latter constitute the objective functions of the multi-objective optimisation problem. The energy efficiency design index, the ratio of the above to below deck number of containers, the required freight rate, the ship’s zero-ballast container capacity and the total ship resistance were used in this study. Genetic algorithms were used for the solution of this multi-objective optimisation problem.