An anatomical study of roots and stems of five self-rooted cherry rootstocks with different growth control potentials was performed to compare their structure and xylem anatomy. The aim was to correlate anatomical parameters with rootstock dwarfing potential and theoretical hydraulic conductance (k h), and to evaluate the potential application of anatomical characteristics in the preselection process for prediction of ultimate tree vigor. One of the mechanisms of water transport efficiency reduction in dwarfing rootstock stems is from the rootstock xylem anatomy. Anatomical parameters of ‘Gisela 5’ and ‘Mazzard’ were typical for dwarfing and vigorous rootstocks, respectively, and were thus suggested as reference rootstocks. Significantly greater vessel diameter and frequency were found in invigorating and dwarfing rootstocks, respectively. Higher k h was obtained in roots, compared to stems, due to significantly larger vascular elements. Dwarfing rootstocks had lower k h due to small vessel lumens and percentage and, to a lesser extent, because of low wood/cortex ratios or percentage of wood. A higher percentage of wood or xylem in cherry roots and stems was not always positively correlated with their conductivity and vigor. Thus, these parameters cannot be reliably used in prediction of the ultimate vigor, although this method was previously suggested for some other fruit tree species. The most reliable anatomical parameters for that purpose proved to be vessel frequency, vessel lumen area, and percentage of vessels on wood cross section. These characteristics could thus be an effective way to estimate dwarfing capacity and could be applied in rootstock selection and breeding programs.