Controlled auto-ignition (CAI) is an advanced combustion technology offering high thermal efficiency and low NOX emissions. One promising approach to achieve CAI combustion is application of negative valve overlap resulting in internal exhaust gas re-circulation. However, combustion control is still an issue which should be resolved before wide application of CAI combustion. Introduction of some degree of fuel stratification via direct fuel injection is interesting approach to control combustion process. In this study a gasoline-fuelled single-cylinder research engine was used to investigate the effects of stratification on combustion and emissions of CAI engine. The stratification was achieved using split direct fuel injection technique, where the second fuel injection controlled the degree of stratification. The results shown that variability of the second injection timing and mass of fuel injected is a viable method to control combustion on-set as well as its duration. However, the trends in both combustion and emissions were found to be non-monotonic, revealing complex relationships between mixture formation and combustion process. It has been found that small degree of mixture stratification delays combustion on-set, whereas large stratification advances combustion. The obtained results confirmed superior combustion controllability via mixture stratification, however with some limitations resulting from reduced efficiency at high degree of stratification. © Published under licence by IOP Publishing Ltd.