Cassava and rice amylopectins and their ϕ,β-limit dextrins were debranched and the unit chain compositions were analyzed by gel permeation chromatography and high performance anion-exchange chromatography. The content of amylose and super-long amylopectin chains was 15.5-15.6% and 0.8-1.2% in cassava and 15.1-18.7% and 3.4-8.6% in rice starches, respectively. The internal unit chain profiles of the amylopectin samples were obtained from the ϕ,β-limit dextrins. Short B-chains were subdivided into a major group (BSmajor) with a degree of polymerization (DP) of 8-25 and a minor group of “fingerprint” B-chains (Bfp) with DP 3-7. Cassava and rice amylopectins possessed different amounts and patterns of Bfp-chains. The rice samples contained higher amounts of Bfp-chains, which suggested larger size of its clusters when compared with cassava. The content of the shortest “fingerprint” A-chains (Afp) was also variable, especially between the rice cultivars. The position of the internal chains in the original amylopectin chain profile was traced. The reconstructed B-chain profiles fitted well with the original profiles. This implied that most of the B-chains carried external chain segments of similar lengths, which corresponded to the experimentally measured average length.