This study relates to a detailed speciation analysis of hydrocarbon emissions from a homogeneous charge compression ignition (HCCI) engine utilizing negative valve overlap (NVO). A split fuel injection technique is employed, where the first injection is applied during exhaust re-compression and the second injection is applied at the beginning of the main compression. Quantities of fuel injected at the two timings are varied, from the whole fuel injection during NVO to the whole fuel injection during the main compression event. These split-fuel ratio sweeps are repeated both for a stoichiometric mixture and for a slightly lean mixture to determine the effect of an excess air ratio on emissions. It has been found that the employed injection strategy has a great impact on hydrocarbon composition in an exhaust gas as a result of the NVO exhaust-fuel reactions. Fuel injection in an early stage of NVO results in an excessive emission of 1,3-butadiene. Additionally, high emissions of methane are observed, but solely in the lean mixture regime.