This work reports on the application of spectroscopic measurements coupled with data processing techniques in order to study, in terms of spectral emissions, the dynamic of the HCCI (Homogeneous charge compression ignition) combustion that occurs inside the combustion chamber of an optically accessible direct injection Diesel engine. A pre-processing of the recorded spectra is required for a correct analysis. The procedure of pre-processing consists of two main steps, that is: noise filtering with a technique based on the POD (Proper Orthogonal Decomposition); estimate and subtraction of the baseline. The analysis of the dynamics of the recorded spectra was carried out by the estimates of the synchronous and asynchronous 2D correlation spectra. These correlation spectra provide information on the correlation of the temporal changes of the spectral intensity among the different bands (or wavelength) of the recorded spectrum; therefore, they provide information on the temporal correlation between the various chemical species that present characteristic bands within the acquisition band. This paper reports on the analysis of the synchronous and asynchronous 2D spectra related to the emission spectra; in particular, attention is focused on the characteristic bands of radicals OH, CH and HCO. The analysis of the emission spectra reported in this work provides information that can be useful for understanding chemical mechanisms related with HCCI combustion.