A set of 13 waxy rice genotypes prepared by chemical-induced mutation of rice variety TNG67 and 7 waxy rice varieties widely grown in Taiwan were compared for structural, rheological and retrogradation characteristics of starches. Wide differences in retrogradation enthalpy (ΔHret), gel firmness and storage modulus (G’ret) were observed for 2-week stored gels of 20 starches. Ratio of short-to-long amylopectin chains was significantly higher (p < 0.05) in starches from mutant genotypes than in commercial varieties. ΔHret and G’ret of starch pastes stored over 4 weeks showed stronger correlation with amylopectin chain-profile compared to those stored for 2 weeks. Amount of long amylopectin chains was correlated positively (p < 0.05) with ΔHret and gel firmness. Overall, ratio of short-to-long amylopectin chains affected almost all the rheological and retrogradation parameters. Results of this study can be useful to plant breeders and food industry for quality improvement and selection of waxy rice mutants for various applications.