Starch granules contain two glucose polymers, amylopectin and amylose. Amylose makes up approximately 10 to 30% (w/w) of all natural starches thus far examined, but mutants of crop and model plants that produce amylose-free starch are generally indistinguishable from their wild-type counterparts with respect to growth, starch content, and granule morphology. Since the function and adaptive significance of amylose are unknown, we asked whether there is natural genetic variation in amylose synthesis within a wild, uncultivated species. We examined polymorphisms among the 1,135 sequenced accessions of Arabidopsis (Arabidopsis thaliana) in GRANULE-BOUND STARCH SYNTHASE (GBSS), encoding the enzyme responsible for amylose synthesis. We identified eighteen accessions that are predicted to have polymorphisms in GBSS that affect protein function, and five of these accessions produced starch with no or extremely low amylose [<0.5% (w/w)]. Eight further accessions had amylose contents that were significantly lower or higher than that of Col-0 [9% (w/w)], ranging from 5 to 12% (w/w). We examined the effect of the polymorphisms on GBSS function and uncovered three mechanisms by which GBSS sequence variation led to different amylose contents: 1) altered GBSS abundance, 2) altered GBSS activity, and 3) altered affinity of GBSS for binding PROTEIN TARGETING TO STARCH 1 (PTST1) – a protein that targets GBSS to starch granules. These findings demonstrate that amylose in leaves is not essential for the viability of some naturally occurring Arabidopsis genotypes, at least over short timescales and under some environmental conditions, and open an opportunity to explore the adaptive significance of amylose.