Global endeavors to reduce emissions in the shipping industry are accelerating the interest in fuel cell system. This paper explores the application of different fuel cell types (LT-PEMFC, HT-PEMFC and SOFC) in combination with different fuels (LH2, LNG, MeOH and NH3) in expedition cruise ships. The goal of this paper is to evaluate the impact of the combination of fuel cell system implementation and operational profile on the design of expedition cruise vessels. Impact is expressed in ship size, capital cost, operational cost and emissions. The impact model takes into account: fuel storage, onboard fuel processing, fuel cell system characteristics, balance of plant components, fuel cost over operational lifetime and emissions of fuel cell & fuel processing. In the research, 7 different fuel cell systems and 3 different hybridization options are considered.@en