Amylopectins were purified from five waxy cereal starches (corn, sorghum, barley, wheat, and rice) in amorphous state by ethanol precipitation from dimethyl-sulfoxide (DMSO) solution followed by removing any amylose complexes with butanol in water. Their molecular weights ( M w) were determined by size-exclusion chromatography in tandem with multi-angle laser light scattering and refractive index detectors. Chain length distributions were determined by debranching followed by size-exclusion chromatography coupled with a refractive index detector. Amylopectin pastes (15% dry solids) were also analyzed using a dynamic rheometer while cooling to 4 °C and storing for 20 days, and the relations between the structural and rheological characteristics were investigated. The weight-average molecular weights ( M w) of the waxy cereal amylopectins ranged from 204.4 × 10 6 to 344.4 × 10 6 g/mol, and the average chain length (CL w) ranged from 26.8 to 30.4. Among the tested starches, waxy rice had the largest amylopectin molecules and the longest B ⩾ 2 chains. The order of chain length of B ⩾ 2 chains among the samples were waxy rice > waxy corn = waxy sorghum > waxy barley = waxy wheat. But there were no difference in the CL w of total chains among the amylopectins. Storage ( G′) and loss ( G″) moduli of amylopectin pastes (15% solids) significantly increased during the cooling period from 95 to 4 °C, which was more than the increase during cold storage for 20 days at 4 °C. Among the waxy samples, waxy rice displayed the greatest moduli increases both during the initial cooling and during the cold storage. Among the structural parameters measured, the M w of amylopectin and CL w of B ⩾ 2 chains correlated positively with complex modulus( G ∗) increases.