The stratification of in-cylinder mixtures appears to be an effective method for managing the combustion process in controlled auto-ignition (CAI) engines. Stratification can be achieved and controlled using various injection strategies such as split fuel injection and the introduction of a portion of fuel directly before the start of combustion. This study investigates the effect of injection timing and the amount of fuel injected for stratification on the combustion and emissions in CAI engine. The experimental research was performed on a single cylinder engine with direct gasoline injection. CAI combustion was achieved using negative valve overlap and exhaust gas trapping. The experiments were performed at constant engine fueling. Intake boost was applied to control the excess air ratio. The results show that the application of the late injection strategy has a significant effect on the heat release process. In general, the later the injection is and the more fuel is injected for stratification, the earlier the auto-ignition occurs. However, the experimental findings reveal that the effect of stratification on combustion duration is much more complex. Changes in combustion are reflected in NOX emissions. The attainable level of stratification is limited by the excessive emission of unburned hydrocarbons, CO and soot