RS2 and RS3 are two of the main resistant starch types in food, and the primary types found in raw and cooked rice respectively. To elucidate the physiochemical determinants for RS2 and RS3 content in rice, this study investigated the fine amylopectin structure, starch granules morphologies and starch pasting properties of nine different rice accessions. The results revealed that not all the accessions showed a decrease in resistant starch after cooking and cooling. Granular size, paste properties, fb1 and fb3 showed a significant negative correlation with RS3, whereas fa showed a significant positive correlation with RS3. RS2 had no significant correlation with granular size, but did have a significant positive correlation with HPV, CPV and fb2. Different rice types could be distinguished by the fine amylopectin structure of DP6-12 and DP13-24 chains. Taken together fa, fb2 and HPV and CPV values may have the potential to be used as indices for distinguishing or characterising rice with different RS2 and RS3 contents.