Amylose content is generally the most important factor determining rice eating and cooking quality. Commercial rice varieties are, in fact, placed into market classes based on having “zero” (0-7%), low (10-20), intermediate (20-25%), or high (>25%) apparent amylose. This study demonstrates that the single-nucleotide polymorphisms (SNP) in the exon 1 (G->T) and in exon 6 (A->C) of GBSS can be used as markers to efficiently distinguish the amylose classes. These two SNPs accounted for 89.2% of the variation in apparent amylose content in a pedigree of 89 US rice varieties and 93.8% of the variation among 279 accessions in a European germplasm collection. All low amylose varieties had the T allele of exon 1. All intermediate amylose varieties had the G allele of exon 1 and the C allele of exon 6. All high amylose varieties had the G allele of exon 1 and the A allele of exon 6. In contrast to previous reports, the amylose content of rice varieties in West Africa was also largely determined by GBSS alleles, which accounted for 93.3% of the variation among 77 samples from West Africa Rice Development Association. GBSS gene from O. glaberrima was found to lack a transposon in exon 10 and have an additional polymorphism (G->A) in exon 12, but these do not significantly alter amylose content. The study also shows that some GBSS genes from high amylose varieties contain an additional C->T polymorphism in exon 10. This SNP does not significantly alter amylose content, but alters rice starch pasting properties. Traditional RVA analysis of starch pasting properties is complicated by differences in the shear forces between samples. However a simple method was developed to overcome this problem and it was shown that starch granules from rice varieties with the T allele of exon 10 are notably more shear resistant. Amylose and the SNP in exons 1, 6 and 10 of GBSS also played a key role in starch re-association. They accounted for 81 and 71.5%, respectively, of the variation in “gel hardness” of RVA samples which have been allowed to incubate at room temperature for 24 hours.