Abstract Biogas is a biofuel which can be used as an energy source for gas-operated vehicles or for electricity and heat production. This paper studies the greenhouse gas emissions from biowaste, waste water treatment plant sludge and agricultural biomass based biogas use as a transportation fuel and compares the transportation use with the electricity and heat production and composting of feedstock. The research is conducted using Life cycle assessment methods and the calculation follow the directive 2009/28/EC, ISO 14040 standard and Greenhouse Gas Protocol. The use of biogas in transportation sector led in all studied cases to reductions of GHG emissions compared to fossil transportation fuels. The GHG reductions varied from 49% to 84%. Biogas production and use in electricity and heat production also led to GHG reductions compared to composting of feedstock but the reductions are not as high as in transportation use in most of cases. In addition if biogas is already used in energy production, it should be considered carefully whether the advantages of directing biogas to transportation purposes are profitable from a GHG emission point of view. However the GHG reductions are heavily depended on local energy systems. This creates challenges for the policy makers and leads to need for system scale comparisons. The wider use of biogas as a transportation fuel has a potential for high GHG emission reductions in the transportation sector.