This study proposes an integrated framework for assessing the efficiency of regional road transport systems in the Balkans that combines operational and environmental performance indicators. The framework uses a Data Envelopment Analysis (DEA) approach to assess various inputs and outputs, including infrastructure, vehicle characteristics, traffic volumes, fuel consumption and pollutant emissions. Particular attention is paid to the inclusion of undesirable outputs such as carbon dioxide and particulate matter emissions in order to accurately capture the environmental impact of transportation activities. The proposed model aims to provide a comprehensive and balanced assessment of transport efficiency, taking into account both operational efficiency and sustainability aspects. By applying this approach to regional road networks in the Balkans, the study provides a methodological basis for policy makers and planners who want to improve the performance of the transport system while minimizing the environmental footprint. This holistic assessment tool can support informed decision-making to promote sustainable regional development and improve the overall resilience of road infrastructure in the region. The results show significant differences in efficiency across the region, with countries such as Slovenia and Greece performing well, while others, such as Albania, show significant inefficiencies. Limitations include the availability and consistency of data between countries, particularly in relation to undesirable outputs. Future research could extend the model to include dynamic variables such as investment trends, policy changes, or the introduction of clean technologies.