Effects of fuel physical and chemical properties on combustion and emissions were investigated on both metal and optical diesel engines. The new generation oxygenated biofuels, n-butanol and DMF (2,5-dimethylfuran) were blended into diesel fuel with 20% volume fraction and termed as Butanol20 and DMF20 respectively. The exhaust gas recirculation (EGR) rates were varied from zero to ∼60% covering both conventional and low temperature combustion. Meanwhile, the reference fuels such as n-heptane, cetane, and iso-cetane were also used to isolate the effects of different fuel properties on combustion and emissions. In addition, to clarify the effects of oxygenated structures on combustion and emissions, a fundamental partially premixed burner was also used. Results based on metal and optical diesel engines show that fuel cetane number is the dominated factor to affect the auto-ignition timing and subsequent combustion process. Fuel other properties have little effects on mixture formation and combustion processes at 20% blending ratio and a medium engine load. DMF20 has higher NOx emissions than the other fuels at lower EGR rates, but the effects of fuel properties on NOx emissions become very small as EGR rates exceed 45%. Fuel properties have little effect on THC and CO emissions in the current conditions and the THC and CO emissions are mainly controlled by EGR. The earlier combustion images for Butanol20 and DMF20 present more blue flames than that of diesel fuel and bio-oxygenated fuels addition leads to lower soot luminosity. DMF20 has lower soot emissions and soot luminosities than those of Butanol20. However, DMF addition results in higher soot volume fractions compared to n-butanol addition by the method of two-color laser induced incandescence on partially premixed laminar flames. Therefore, it can be concluded that in the view of fuel oxygenated structure, n-butanol is better on soot reduction than DMF, while the lower cetane number of DMF can result in lower soot emissions in real diesel engine conditions.