This paper reviews the current general understanding of fuel effects on combustion and emissions, fuel processing, and emission control technologies and assesses areas of opportunity in further research in clean diesel systems. The critical basic research areas identified focus on fundamental processes mat would develop a scientific knowledge base for the long-term development of clean diesel technology. The suggested approach, from a basic research perspective, will complement other pragmatic development programs in clean fuels production, application, engine and emission control technologies. Among areas suggested are: studies in developing basic data and modeling of fuel chemistry and emission mechanisms both in cylinder and during after-treatment, interactions of new fuel and engine technologies, gas-to-liquid fuel processing and utilization, and detailed particulate emission characterization and their health effects. The health effect benefits from clean fuels may be more than proportional to the reduction in mass emissions.