The U.S. Department of Energy (DOE) is embarking on a program investigating the use of Fischer-Tropsch (FT) fuels as a premium quality substitute or blending agent in direct-injection compression-ignition (diesel) engines. This paper aims to direct attention to the processing of FT fuels, emissions issues, available engine technology and the opportunity offered by FT diesel fuels for emissions control when considering diesel injection techniques. In modern automotive and heavy duty direct-injected (DI) diesel engines, precise fuel injection control is critical for achievement of 1998 and 2004 NOX and PM emission levels. High injection pressures, pilot injection and injection rate shaping are all optimized to maximize efficiency and power and to minimize emissions. These parameters must be considered as variables in the trade-off scenario between NOX and PM. Another parameter that may be considered important is the fuel type. Fischer Tropsch (F-T) liquid fuels produced from synthesis gas (a mixture of carbon monoxide and hydrogen) are straight chain aliphatic hydrocarbons containing virtually no aromatic compounds or sulfur species. F-T liquid fuels offer such significantly different chemistry that when compared to typical petroleum based diesel fuels, a new PM versus NOX variable emerges.