The influence of root system and genotype on vegetative and reproductive growth was characterized on untrained apple (Malus domestica) genotypes that were own-rooted or grafted onto M.9 rootstock. The eight genotypes assessed were selected at INRA for resistance to scab (Venturia inaequalis) and low susceptibility to mildew (Podosphera leucotricha), good fruit quality and aptitude to storage, and depending on genotype, other traits such as regular bearing and one fruit per inflorescence. The two main objectives were to determine the influence of (1) the scion genotype, and (2) the root system genotype on tree growth and yield. Trunk cross-sectional area (TCSA), branch cross-sectional area (BCSA) and position of branches with a basal diameter of more than one centimeter were measured at the end of the third year of growth in the orchard. Yield and fruit size data were collected during the first four years of tree growth. Different genotypes had different TCSA and total BCSA but all had a smaller TCSA and total BCSA when grown on M.9 compared with own-rooted trees. The relationship between TCSA and total BCSA was also different depending on genotype but remained unaffected by root system. The relative location of BCSA, or basitony of the trunk, was influenced by the type of root system. Own-rooted trees were more basitonic than trees on M.9. Yield, precocity and fruit size differences were attributed to both genotype and root system. In all genotypes, yield efficiency (kg of fruit/cm2 TCSA) was higher with M.9. This may not be the defining characteristic since some genotypes expressed similar or even higher yields and fruit size in the 3rd and/or 4th year when own-rooted. Precocious own-rooted trees, which in our study belong to type IV architectural class (acrotonic), may be more interesting in the long-term because, although they have later entrance into production, they may have higher cumulative yields as early as the 4th year, and a better distribution of fruit within the canopy.