The relationships were determined between molecular properties of amylopectin, a hyperbranched glucose polymer and the major component of starch, and higher-level structures in native starch (double helices, crystallinity and crystalline amorphous lamellae). Parameters from NMR, differential scanning calorimetry, and size exclusion chromatography of beta-limit dextrins of a series of waxy starches, together with literature data, gave information on relationships between the structure of the interior of the amylopectin molecule and crystallinity. The structure of internal B chains (those with one or more branches) of amylopectin influences both crystalline properties and crystallinity. More B chains produce larger crystalline amorphous lamellae, probably by expanding the amorphous lamellae, while larger B chains increase the ability of annealing to increase order through greater mobility for the chains to rearrange at higher temperatures. This study brings into question the common assumption that A chains (unbranched chains) are necessarily smaller than B chains.