The origins and biogeographical history of Vitis vinifera L. (domesticated grapevine) remain largely unknown. Shape and size have long been used as criteria to distinguish between wild and domesticated grape pips. Here we have analyzed variations of seed morphology in order to provide accurate criteria for the discrimination of different groups of varieties. Diversity in present-day cultivars and wild grapevines of Greek and east Mediterranean origin in relation to other Asiatic and European varieties and wild grapevines provides the basis for our analysis, which aims to allow the characterization of the ancient diversity of cultivated grapes in relation to present-day cultivars. Geometric morphometric analyses (Elliptic Fourier Transform method) have been used to characterize the seed shape and size of modern and archaeological material using 40 variables per seed. 197 archaeological grape pips from the 7th century BC sanctuary of Hera in Samos, Greece were compared with an extended reference collection of 269 modern cultivars and 83 wild populations, 10,518 seeds in total. Our study confirms the relationships between seed shape and domestica-tion. Modern diversity is partly structured by the geographical origin of cultivars, but influence of other factors may play a significant role in clustering. The wide diversity of varieties offered at the Heraion of Samos during the Archaic Period, including cultivars growing on the island, imported grapes and wild morphotypes, is related to the history and geographical location of the island as well as to the diversity in the geographical range of pilgrims making offerings to the sanctuary.