The potential future role of different biofuels, hydrogen, and so-called electrofuels/power-to-X (produced by electricity, water, and carbon dioxide, CO2) in different transportation sectors remains uncertain. The CO2 abatement cost, i.e., the cost for reducing a certain amount of greenhouse gas (GHG) emissions, is central from a societal and business perspective, the latter specifically in the case of an emission reduction obligation system (like in Germany and Sweden). The abatement cost of a specific fuel value chain depends on the production cost and the GHG reduction provided by the fuel. This paper analyses the CO2 abatement costs for different types of biofuels, biomass-based jet fuels and electrofuels for road transport and aviation, relevant for the Swedish and EU context. Since most assessed alternative fuel pathways achieve substantial GHG emission reduction compared to fossil fuels, the fuel production cost is, in general, more important to achieve a low CO2 abatement cost. The estimated CO2 abatement cost ranges from -0.37 to 4.03 SEK/kgCO2 equivalent. Fuels based on waste feedstock, have a relatively low CO2 abatement cost. Fuel pathways based on electricity or electricity and biomass have relatively high CO2 abatement cost. The CO2 abatement cost for lignocellulosic based pathways generally ends up in between.