The transportation sector is one of the largest sources of EU’s greenhouse gas emissions. In 2011, transportation represented approximately 25 percent of total EU’s greenhouse gas emissions. Urban mobility accounts for 40% of all CO2 emissions of road transport and up to 70% of other pollutants from transport. As, transportation and mobility play a crucial part both in urban economics and the quality of life, it is of great significance to ensure a low carbon transportation sector, so as to deal with the threat that climate change poses to urban areas. This study examines the factors that affect the production of carbon dioxide (CO2) as well as of air pollutants, in 9 major European cities, aiming to provide a comprehensive overview of the actual knowledge on the atmospheric pollution from public transportation systems. CO2 emissions as well as air pollutants, such as CO, HC, PM, NOx are calculated for the diesel and CNG bus fleets of the European cities under study. Finally the environmental benefits, in terms of CO2 and CO, HC, PM, NOx emissions reductions, from the penetration of different biodiesel blends (from B10 to B100) to the bus fleets are estimated.