Homogeneous charge compression ignition (HCCI) combustion applied to the internal combustion engine presents several advantages to meet current automotive objectives. However, controlling the progress of this combustion mode is inherently challenging. This study proposes to use ozone, a strong oxidizer, to control combustion. Experiments were carried out on a HCCI engine fueled with primary reference fuels (PRFs) and seeded in the intake by ozone. Results are presented for six different PRFs, and the effect of ozone on their combustion progress was investigated. Simulations in a constant volume reactor were also performed to explain the effect of ozone based on the chemical kinetics.