Two peach cultivars, i.e. ‘Andross’ and ‘Mercil’ were budded onto four rootstocks of varying vigor (‘Garnem’, ‘GF 677’, ‘Rootpac R’ (RPR) and ‘Rootpac 20’ (RP20)) and planted in pots. The plants were grown for three years, and each year the growth of the trees (in terms of trunk cross sectional area, tree height, and shoot length), fruit production and leaf nutrient concentration were assessed. The rootstock exerted a significant effect on the above-measured variables, as the lowest tree height in both cultivars was recorded when these were grafted on RP20 (the most dwarfing rootstock of all four used). The yield per tree was highest when the most vigorous rootstocks. ‘Garnem’ resulted in the highest upper plant dry weight, while ‘RP20’ in the lowest. Cultivar exhibited a significant effect regarding leaf nutrient concentration, as ‘Andross’ presented higher concentrations of N, K, Ca and Fe in most combinations and lower concentrations of P and Cu. The discriminant analysis, using all growth and nutrient data from the last two years, revealed that irrespective of the cultivar budded, ‘RP20’ and ‘GF 677’ were clearly distinguished from each other and from ‘RPR’ and ‘Garnem’. On the other hand, the hierarchical agglomerative analysis pointed out the crucial role of ‘RP20’ and ‘Garnem’ on tree growth and leaf nutrient concentration, with the cultivar budded on them playing a minor role. In conclusion, the fertilization program of a young, newly established orchard, should take into account the singularity of each scion-rootstock combination, to achieve the optimum tree performance.