The external profile of seeds is a good phenotypic descriptor, indicative of the origin and diffusion of grape vines (Vitis vinifera L.) over the centuries. Archaeological seeds conserved in an anaerobic environment after discovery were compared with modern seeds, belonging to eleven autochthonous cultivars, sampled in Tuscan vineyards. To study seed profiles we used geometric morphometric analysis (elliptical Fourier analysis) combined with multivariate statistical methods. When the values obtained were entered in a database, they produced a cladogram based on Euclidean distances between varieties of archaeological and modern vines, showing that seeds belonging to the same group had phenotypic affinities.