Wheat and barley are two of the founder crops domesticated in the Fertile Crescent, and currently represent crops of major economic importance in temperate regions. Due to impacts on yield, quality and end-use, grain morphometric traits remain an important goal for modern breeding programmes and are believed to have been selected for by human populations. To directly and accurately assess the 3D characteristics of grains, we combine X-ray micro computed tomography (µCT) imaging techniques with bespoke image analysis tools and mathematical modelling to investigate how grain size and shape varies across wild and domesticated wheat and barley. We find that grain depth, and to a lesser extent width, are a major driver of shape change and that these are still relatively plastic traits in modern bread wheat varieties. Significant changes in grain depth are also observed to be associated with differences in ploidy. Finally, we present a model that can accurately predict the wild or domesticated status of a grain from a given taxa based on the relationship between three morphometric parameters (length, width and depth) and suggest its general applicability to both archaeological identification studies and breeding programmes. This article is protected by copyright. All rights reserved.