Low temperature combustion engine technologies are being investigated for high efficiency and low emissions. However, such engine technologies often produce higher engine-out hydrocarbon (HC) and carbon monoxide (CO) emissions, and their operating range is limited by the fuel properties. In this study, two different fuels, a US market gasoline containing 10% ethanol (RON 92 E10) and a higher reactivity gasoline (RON 80 E0), were compared on Delphi’s second generation Gasoline Direct-Injection Compression Ignition (Gen 2.0 GDCI) multi-cylinder engine. The engine was evaluated at three operating points ranging from a light load condition (800 rpm/2 bar IMEPg) to medium load conditions (1500 rpm/6 bar and 2000 rpm/10 bar IMEPg). The engine was equipped with two oxidation catalysts, between which was located the exhaust gas recirculation (EGR) inlet. Samples were taken at engine-out, between the catalysts, and at tailpipe locations. In addition, part of the raw exhaust was diluted and sampled for HC speciation. Canisters and sorbent membranes were used to collect volatile HCs and semi-volatile HCs, respectively. Di-nitrophenyl hydrazine (DNPH) cartridges were also used for collecting oxygenated species. Results showed overall lower HC emissions with the RON 80 E0 fuel compared to the RON 92 E10 fuel. For both fuels, the percentage of aromatic HCs was higher in the exhaust than in the fuels themselves. High aldehyde and ketone emissions were observed for both fuels. Detailed exhaust HC speciation can provide valuable information for modeling GDCI processes and eventually for determining the optimum combustion control methodologies to increase combustion efficiency and lower engine-out CO and HC emissions. In addition, HC speciation is useful for the development of robust emission control systems.