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This paper discusses the effects of stroke-to-bore (S/B) ratio on HCCI combustion. KIVA-3V, coupled with a multi-zone detailed chemical kinetics solver, is used to quantify the effects of changes in S/B ratio to heat transfer, thermal stratification and HCCI combustion. Three S/B ratios (0 5, 1.1 and 1.5) are analyzed. The results indicate that a cylinder with smaller S/B has more heat losses and lower thermal efficiency compared with a cylinder with larger S/B ratio, because of larger area-to-volume ratio near TDC. Moreover, the lowest S/B ratio case has a narrower temperature distribution before the onset of combustion. This leads to shorter burn duration, higher heat release rate and, consequently, increased knocking tendency. The emission results also favor the higher S/B ratio, with S/B=0.5 having the highest CO and HC emissions for relatively early combustion phasing; however, this trend is reversed as combustion is retarded.