Genomic approaches can help to understand the molecular basis of somatic variation in grapevine. We have analyzed a new white berry somatic variant of Tempranillo that allowed the development of the new cultivar Tempranillo Blanco with very good features for the elaboration of white wines. Comparative genomic DNA hybridizations to microarrays as well as whole genome sequencing indicated that Tempranillo Blanco bears chromosomal reorganizations and deletions affecting both linkage groups 2 and 5. Deletion on linkage group 2 extends over 4 Mb and is responsible for several hundred annotated genes in the region to be hemizygous in this cultivar (almost one fourth of the linkage group and 1% of the whole genome). Among them, the complex color locus in linkage group 2 has lost the functional alleles at both MybA1 and MybA2 genes giving rise to the loss of berry pigmentation. The presence of this deletion also affects transmission of the corresponding chromosome in self progenies of Tempranillo Blanco. Similar analyses using comparative genomic hybridizations of other white derivative cultivars such as Garnacha (Grenache) Blanca and Mazuelo (Carignan) Blanco also identified the presence of deletions, with different sizes in each case, affecting the color locus on linkage group 2. Altogether, these results demonstrate the presence of mitotic chromosomal rearrangements accumulating in grapevine cultivars that are vegetatively propagated for centuries. Some of them, causing loss of genetic material, could be responsible for part of the observed somatic variation.