The starch synthase IIa (SSIIa) gene of rice (Oryza sativa L.) has been shown to be the alk gene that controls alkali disintegration of rice grains, although the effects of naturally occurring alk mutant alleles on enzyme function have yet to be determined. We genotyped 60 rice cultivars for two single-nucleotide polymorphisms (SNPs) in rice SSIIa, including one that results in an amino acid substitution. Incorporating data for three other SNPs previously genotyped in rice SSIIa, five haplotypes were found. We analysed the association of these SSIIa haplotypes with the chain-length distribution of amylopectin, the gelatinisation temperature of rice flour, the alkali spreading score, and the starch association of the enzyme. It was determined that two SNPs resulting in amino acid changes close to the C-terminus most likely alter SSIIa both in terms of activity and starch granule association. This in turn alters the branch-length distribution of amylopectin and the gelatinisation properties of starch.