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Concentrations of hydroxyl radicals and formaldehyde were calculated using homogeneous (HRM) and stochastic reactor models (SRM), and the result was compared to LIF-measurements from an optically accessed iso-octane / n-heptane fuelled homogeneous charge compression ignition (HCCI) engine. The comparison was at first conducted from averaged total concentrations / signal strengths over the entire combustion volume, which showed a good qualitative agreement between experiments and calculations. Time- and the calculation inlet temperature resolved concentrations of formaldehyde and hydroxyl radicals obtained through HRM are presented. Probability density plots (PDPs) through SRM calculations and LIF-measurements are presented and compared, showing a very good agreement considering their delicate and sensitive nature.