The diesel combustion process involves complex physical and chemical processes. Given this complexity it is not surprising that a wide range of fuel effects on emissions are reported in the literature. In the European Auto/Oil study the EPEFE programme showed that interactions between fuel and engine hardware could partially explain the observed emissions effects. Variations in fuel physical properties can lead to variations in injection timing, fuel delivery, exhaust gas recirculation (EGR) and other parameters. To understand fuel effects on emissions it is clear that we need to separate these different mechanisms.In this programme a modem, electronically controlled, direct-injection (DI) passenger car engine has been studied using a sophisticated test bed system which makes it possible to monitor and control all key engine variables. Seven fuels were tested, including four varying in density and poly-aromatics content taken from the EPEFE programme. In the first stage the engine was run with its controls in the normal production configuration. Fuel effects on emissions were consistent with results from a similar engine/vehicle tested over the European emissions drive cycle. However, substantial changes in engine calibration settings (primarily EGR rate and injection timing) were found to be occurring, despite sophisticated control of both parameters. In the second stage EGR rate and timing were maintained at the manufacturer's intended settings by using a modified control system. Fuel effects on emissions were now found to be substantially different. For example, the effect of increasing density on NOx emissions was reversed, with the 8% reduction seen in the first stage replaced by a 3% increase.These results confirmed that fuel effects on engine calibration were major contributors to the emissions effects observed when the engine was tested in its normal production configuration. Only by controlling, these variables can true fuel effects on in-cylinder processes be studied.