The organogenesis potential is different among cultivars and must be optimized for individual genotype. Shoot organogenesis capacity from in vitro leaves and root organogenesis capacity of in vitro shoots in six clonal apple rootstock cultivars were compared. The shoot organogenesis capacity was highly genotype dependent. ‘GM256’ was found to be the most responsive genotype for shoot regeneration from leaf explants among the cultivars, showing high regeneration percentage on all tested media. The effects of basal medium composition and cytokinins on shoot regeneration were different depending on rootstock genotype. Optimum regeneration occurred on Murashige and Skoog (MS) basal medium for ‘71-3-150’, and optimum regeneration occurred on Quoirin and Lepoivre (QL) basal medium for ‘60-160’ and ‘ПБ’. Thidiazuron (TDZ) was more effective than 6-benzylaminopurine (BA) for Malus prunifolia (Y), whereas TDZ and BA were not significantly different for the other cultivars. All rootstock cultivars showed high root organogenic capacity. The percentage of rooting reached more than 90% and the mean root number per plantlet ranged from three to five. The optimum rooting medium was different for different rootstock cultivars. Optimum root organogenesis occurred on half-strength QL medium for ‘GM256’ and ‘Y’, and for ‘ПБ’ and ‘JM7’ on one-quarter-strength MS medium.