A set of 13 waxy rice genotypes prepared by chemically-induced mutation of non-waxy rice variety TNG67 and 7 waxy rice varieties widely planted in Taiwan were screened for various structural and gelatinization properties of starches. Wide variation on physicochemical properties and molecular structure of amylopectin for the 20 waxy rice starches were obtained and relationship between gelatinization properties and molecular structure of starch were discussed. More attributes on swelling and gelatinization thermal properties, comparing to pasting attributes, showed significant correlation with molecular structure parameters. The swelling and gelatinization thermal properties of waxy rice starch did not show significant correlation with molecular size of amylopectin, while significant correlations were found between the swelling or gelatinization thermal properties and chain length of amylopectin. Results suggest that the swelling and pasting of waxy starch is essentially dominated by granule architecture and is dependent on the interactions among amylopectin chains.