The economic consequences of road traffic injuries (RTIs) are very important in terms of health care costs. The aim of this study is to provide estimates of health care costs of non-fatal RTIs and to estimate functional outcomes using in-hospital rehabilitation data. We identified all emergency department (ED) visits related to RTI during 2008 and then linked them with hospital discharges and rehabilitation admissions, health care costs following RTI were estimated from the integrated database. We performed an epidemiological evaluation of RTI with a comprehensive description of functional outcomes at 6 months. Health care costs have been estimated at about €80 million with a per person cost of €522. About 18% of the total cost was due to rehabilitation treatments. In multivariate analysis the variables that correlated better with higher total health care costs were: older age, injury severity, presence of spinal lesion. Patients requiring rehabilitation were: the elderly, patients suffering from a spinal cord injury and leg injuries. This study provides consistent health care cost estimates of RTI using administrative databases and it shows a picture of functional outcomes after RTI. Further research is needed for the estimation of other components of the total cost of RTI.