This research investigates the effects of a synthetic diesel-like fuel (Fischer-Tropsch diesel) and biofuels (ethanol and biodiesel) fuel blends on the energy-exergy efficiencies and gaseous exhaust emissions characteristics of a compression ignition engine. Two blends of alternative fuels denoted as E15B35FTD50 (15% ethanol, 35% biodiesel, and 50% Fischer-Tropsch diesel) and E15B35D50 (15% ethanol, 35% biodiesel, and 50% diesel) were experimentally studied on a single-cylinder diesel engine and compared to diesel fuel. The results show that the energetic and the exergetic efficiencies of the alternative fuels are comparable to those of the engine fueled with diesel fuel. The unburnt HC, NO, N2O, and NH3 emissions were reduced for the two alternative fuel blends compared to diesel, while CO emissions increased. The light HC species were found to slightly increase for the alternative fuel blends in comparison with diesel fuel. However, the total HC was considerably reduced by the combustion of E15B35FTD50 not only when compared to the diesel fuel combustion, but also when compared to E15B35D50. Overall, these results may contribute to identifying advantages and limitations in terms of energetic-exergetic analysis and emissions for the new generation of conventional diesel and hybrid electric vehicles that aim to achieve future emissions regulations.