The barley (Hordeum vulgare) gene Hv.AGP.S.1 produces two different transcripts encoding small subunits (SSUs) of ADP-glucose pyrophosphorylase (AGPase). It was shown previously that one of these transcripts, Hv.1a, encodes the cytosolic SSU in the endosperm. It is shown here that the other transcript produced from Hv.AGP.S.1, Hv.1b, encodes a plastidial SSU that is required for >90% of the AGPase activity in the leaves. Thus, both of the alternative transcripts encoded by Hv.AGP.S.1 are physiologically relevant: One is important for starch synthesis in the endosperm and the other for starch synthesis in the leaves. Although the Hv.1b transcript is abundant in embryos and present in endosperm, there is no evidence that a protein is produced from this transcript in these organs. This suggests that some, as yet unidentified, post-transcriptional control mechanism prevents the accumulation of the protein encoded by Hv.1b in embryos and endosperm but not in leaves. There is one other known gene in barley, Hv.AGP.S.2, encoding a SSU of AGPase. This gene has been shown to be responsible for the plastidial SSU in the endosperm. It is shown here that Hv.AGP.S.2 probably also makes some contribution to the SSU of AGPase in the leaves and may be responsible for most or all of the plastidial SSU in a range of non-photosynthetic plant organs including the embryo.