Increasing amount of shipboard emissions, and emission regulations entered into force encourage emission reduction technologies to be developed, and new methods to be used. Alternative fuel use as a fuel on marine diesel engines is one of the new methods to reduce shipboard emissions. Methanol and ethanol can be used as a liquid fuel or liquefied natural gas and hydrogen can be used as a gaseous fuel on ships. Aim of this study is to make scientific comparison of alternative fuels which can be used at ships. The environmental and economical performance of methanol, ethanol, liquefied natural gas, and hydrogen were compared. Comparison was made by eleven comparison criterions from different aspects. The most suitable alternative fuel which can be used on ships is determined by defining evaluation scale points for each comparison criterions. Analytic hierarchy process was used to find the weighing of comparison criterions according to given points by five experts to each criterions. Final comparison table is formed including all comparison criterions with given evaluation scale points of each alternative fuels, and weighing for each criterion depend on their importance at maritime sector. Methanol and ethanol, liquefied natural gas, and hydrogen get comparison points of 2.129, 4.092 and 3.796 respectively from the total point of 5.005. Comparison shows that methanol and ethanol do not seem to be preferable to use onboard due to their inadequacy which are investigated in the study. Liquefied natural gas gets the highest total evaluation point in the study, and the most suitable alternative fuel. Hydrogen gets the highest point at safety, bunker capability, durability, adaptability to existing ships, and commercial effects criterions. This study shows that hydrogen can be the alternative to liquefied natural gas used as a fuel at ships, but it requires more studies and improvement on the comply with emission regulations and effect on engine components issues. (C) 2015 Elsevier Ltd. All rights reserved.