Refinements were made to a post-processing technique, termed the Thermal Stratification Analysis (TSA), that couples the mass fraction burned data to ignition timing predictions from the autoignition integral to calculate an apparent temperature distribution from an experimental HCCI data point. Specifically, the analysis is expanded to include all of the mass in the cylinder by fitting the unburned mass with an exponential function, characteristic of the wall-affected region.The analysis-derived temperature distributions are then validated in two ways. First, the output data from CFD simulations are processed with the Thermal Stratification Analysis and the calculated temperature distributions are compared to the known CFD distributions. The results show very good agreement between the calculated TSA and known CFD distributions, except at the leading (hottest) edge where the CFD distributions exhibit a discrete step change and the calculated TSA distributions show a smooth progression. Next, the analysis-derived temperature distributions are compared to optically measured distributions calculated from PLIF images. The calculated distributions agree very well with the optically measured distributions at TDC and around the phasing of the combustion event.Finally, an intake temperature (or combustion phasing) sweep is processed with the TSA and the results show that the higher intake temperature (and earlier phased) conditions have a much wider distribution due to the increasing difference between the gas temperature and the wall temperature and possibly the increasing in-cylinder turbulence as combustion phasing advances toward TDC.