The relationship between the slow digestion property of cooked maize starch and its molecular fine structure was investigated. Results of the in vitro Englyst assay showed a range of rapidly digestible starch (RDS) (70.1-98.9%), slowly digestible starch (SDS) (0.2-20.3%), and resistant starch (RS) (0.0-13.7%) among the tested maize mutant flour samples. Further analysis showed that amylose content was significantly correlated ( R = 0.763, P < 0.001) with RS amount but not with that of SDS, indicating that amylopectin is the starch molecule associated with SDS. Total starch debranching analysis revealed a parabolic relationship between SDS content and the weight ratio of amylopectin short chains (DP < 13, named SF) to long chains (DP >/= 13, named LF), which means amylopectin with a higher amount of either short chains or long chains can produce relatively high amounts of SDS. Furthermore, debranching analysis of the SDS materials from samples with the highest and lowest weight ratios of SF/LF (both had a high amount SDS) showed significantly different profiles, indicating there is not a uniform molecular structure for SDS. Thus, genetic mutants of maize samples have a good potential to provide raw starch materials of high nutritional quality. An additional finding showed that a simple and comparably high-throughput technique of Rapid Visco-Analyzer (RVA) can be used to screen genetic mutants on the basis of their RVA profiles.