The influence of the molecular structure of hydrocarbon fuels on soot, SOF, and NOx emissions from a diesel engine was analyzed while ignition delay and other physical fuel properties were kept constant. Mixtures of normal paraffin (n-tetradecane) and iso-paraffin (heptamethylnonane) were used as a base fuel and one of 5 kinds of hydrocarbons including mono-aromatic, di-aromatic, and non-aromatic was added. The aromatic content varied in the range of 0-60 vol % for the mono-aromatic fuels and 0-40 vol % for the di-aromatic fuels. The experimental results showed that regardless of the molecular structure of the fuel, both particulate and NOx emissions increased linearly with the C/H atomic ratio of the fuels under constant ignition lag. The increase in particulate emissions with C/H atomic ratio was caused by increases in dry soot. The SOF, THC, and BSEC were little affected by the C/H atomic ratio and molecular structure of the fuels. The fuel properties discussed here showed similar results in both DI and IDI engines.