This paper presents an analysis of combustion phasing in a controlled auto-ignition (CAI) engine fuelled with gasoline. Auto-ignition was achieved using an exhaust gas trapping method via negative valve overlap (NVO). Under slightly lean mixture conditions variable intake and exhaust valves timings were applied in order to analyze influence of amount of retained exhaust on auto-ignition timing and combustion duration. Combustion on-set was independent of exhaust valve closing event, which was responsible for amount of trapped residuals. However, it was found that auto-ignition timing was determined by intake valve timing. Combustion duration was affected by both exhaust and intake valve timings. Direct injection allowed for application of different mixture formation strategies including in-cylinder fuel reforming during the NVO phase. When fuel was injected in the late stage of NVO increase of air-fuel ratio (AFR) caused a retard of auto-ignition and reduction of heat release rate. In contrast, opposite effect of AFR was observed if fuel was injected in the early stage of NVO, which resulted in its reforming. Increasing oxygen content during NVO influenced effects of reforming, thus determining combustion course. Split fuel injection, where the first injection timing was set constant in the NVO phase and the second fuel dose was injected during an intake process, allowed for improvement of engine thermal efficiency and exhaust emissions. Injection of the second fuel dose during a compression stroke resulted in advance of auto-ignition due to mixture stratification. However, at slightly lean mixture, stratification led to excessive emission of CO and drop of thermal efficiency.