Recombinant plant-derived pharmaceuticals have been investigated for the last two decades and some products will soon be brought to market. Since veterinary pharmaceuticals seem to be the front-runners of plant-derived vaccines, we selected one model subunit vaccine, the structural capsid protein VP60 against rabbit haemorrhagic disease, and analyzed the expression of three different sequences representing the VP60 open reading frame in potato plants. The generation of antigenic VP60 molecules in the leaf and tuber tissue of potato was tremendously enhanced by replacing virus-derived sequences with plant-optimized codons. In order to identify potentially undesirable alterations in the composition of these genetically modified food components, we studied their nutrient composition and nutritional value in comparison to two parental conventional breeding varieties (Albatros and Desiree). The largest differences in nutrient composition were found between the two conventional breeds and between conventional Desiree and its near-isogenic genetically modified potato plant, indicating that genetic modification as well as conventional breeding can influence nutrient composition. Nevertheless, most parameters of nutritional value seemed to be more affected by conventional breeding than by genetic modification.