Different pathways and technologies can be used to convert woody biomass to transport services, but the biomass use and climate implications vary strongly between the alternatives. This study focuses on primary energy use and climate change effects of using bioenergy for transportation in the context of a renewable-based energy system. Integrated pathways to improve the energy efficiency of power and transportation sectors and integrated intermittent renewable energy are considered. The results show that the bioenergy pathway that produces biomotor fuels to replace fossil fuels leads to high primary energy use and instantaneous biogenic CO2 emission per km of driving distance, thus increasing global warming during the first 40-50 years, compared to fossil alternatives. The electric vehicle pathway using bioelectricity from combined heat and power plants leads to immediate global cooling and much greater climate benefits in the long run compared to biomotor fuels. Climate change effects of light-duty vehicles could be strongly reduced by changes in technology together with system integration that links the transport sector to the electricity and heating sectors. The use of biomass should be considered in the context of the overall integrated energy system, and in relation to the development of energy conversion technologies between different sectors. (C) 2016 Elsevier Ltd. All rights reserved.