In this study, a combustion analysis has been performed in a cylinder of a four stroke engine's mixture by using Fluent and Chemkin commercial codes for CFD analysis. The analysis includes two strokes and provides all the data at compression, combustion and expansion times. An experimental model of an HCCI engine has been used for the in-cylinder combustion analysis. The data obtained at the end of the in-cylinder combustion analysis were compared against the experimental results, and the accuracy of the analysis was investigated. After the validation, it was seen that analytical results agree with the experimental observations. Investigation of the analysis leads to a number of unmeasured chemical reactions and combustion products were investigated.