Reports have stated that Fischer Tropsch (FT) fuels are high quality, low emission diesel fuel substitutes. The purpose of this study is compare the emissions from a heavy-duty, Valmet, diesel engine running on a commercial available FT fuel, Eco-Partm, with the emissions obtained when the same engine is running on a low sulfur diesel fuel with low aromatic content, Swedish environmental class 1 (EC-1) diesel fuel. The two fuels have been analyzed by Fourier transform infrared spectroscopy and Raman Fourier transform infrared spectroscopy. The analyses showed that main constituents in the two fuels are alkanes with no substituents. No aromates or olefines could be detected. A small difference, later verified by gas chromatographic analyses, was noted; the Swedish EC-1 fuel consisted of a larger portion of straight chain, heavier hydrocarbons while the FT fuel consisted of more branched hydrocarbons. The overall impression of the emission analyses is that Eco-Partm gives lower emission than the EC-1 fuel during the modes employed in the ISO 8178 test. Emissions of acetaldehyde, benzaldehyde and acrolein were generally decreased 3-6 times when using FT fuel instead of EC-1 fuel while the emission of formaldehyde was unaffected. Fifteen volatile organic hydrocarbons were also included in the investigation-ethane, ethene, acetylene, propane, propene, propyne, propadiene, isobutene, isobutene, 1-butene, 1,3-butadiene, benzene, toluene, O-xylene and M-xylene. The emissions of the fifteen mentioned hydrocarbons were reduced between 20% - 93% when using Eco-Partm instead of EC-1. Measurements of the regulated emissions during an ISO 8178 test confirmed the obtained results; the emissions of total hydrocarbon (HC) decreased approx. 14% while the emissions of carbon monoxide, CO, and nitrogen oxides, NOx were almost unaffected. The test results in this investigation may indicate that diesel engines running on Eco-Partm can have a lower impact on environment and health than the, in Sweden, commonly used EC-1 fuel.