Tracer-based PLIF temperature diagnostics have been used to study the distribution and evolution of naturally occurring thermal stratification (TS) in an HCCI engine under fired and motored operation. PLIF measurements, performed with two excitation wavelengths (277, 308 nm) and 3-pentanone as a tracer, allowed investigation of TS development under relevant fired conditions. Two-line PLIF measurements of temperature and composition were first performed to track the mixing of the fresh charge and hot residuals during intake and early compression strokes. Results showed that mixing occurs rapidly with no measureable mixture stratification remaining by early compression (220°CA aTDC), confirming that the residual mixing is not a leading cause of thermal stratification for low-residual (4-6%) engines with conventional valve timing.In the second part of the study, single-line PLIF measurements performed later in the compression stroke showed that the distribution of TS and its development are very similar for both motored and fired operation. This finding indicates that the mechanism producing the temperature stratification is the same for both cases, although some differences in magnitude can occur. A subsequent parametric study proved that these differences can be attributed to the impact of both incomplete fuel mixing and cylinder-wall temperature variation, depending on the type of engine operation (DI skipfiring or premixed continuous firing respectively).In the final part of this study, the simultaneous use of the two lasers allowed correlation of the high temperature zones existing before TDC with the early reaction zones after TDC. These image pairs indicated that the first combustion reactions begin in the highest temperature regions followed by reactions in progressively cooler zones, proving that TS is the root cause of sequential auto-ignition in HCCI-combustion engines. All these measurements demonstrate the feasibility of quantitative tracer-based PLIF diagnostics in harsh engine environments and provide useful information for future HCCI engine development.