The transportation of freight by land, sea and air underpins the complex network of global trade in physical commodities. Greenhouse gas emissions from freight transportation are a significant component of global emissions and are predicted to grow in coming decades. However, the inclusion of freight transport in emissions accounts and environmental impact studies is often incomplete. Both data availability and difficulties in allocating freight emissions to specific commodity trades contributes to this. In this study, international freight movements by transport mode are estimated from the bottom-up by imputing global freight transport routes. Emissions are estimated from these freight movements and integrated with a global multiregional input-output model. This enables the calculation of carbon footprints that are complete with respect to freight emissions. We estimate that global freight transport emissions contributed 2.8 Gt CO2-equiv in 2012, or about 41% of total transport emissions. In general, freight footprints contribute about 9% to national emissions footprints. While trade in physical commodities (such as construction materials, food and fossil fuels) are associated with the largest embodied freight emissions, services (such as public administration, education and health) also require significant freight transport. Using a consumption-based allocation of freight transport emissions allows the decarbonisation of other sectors to be complementary to the decarbonisation of transport through reduction in demand, for example through material efficiency strategies. To drive decarbonisation in maritime transport it is critical to include bunker emissions in national emissions inventories, thereby completing the system boundary.