Rootstocks may offer a potential mechanism to influence canopy dynamics for a given scion, mainly in regards to soil moisture. Although the rootstock-scion interaction in grafted grapevines is extensively investigated, the effect of cultivar on root morphology has not been widely tested under field conditions. In the current study, root morphology was compared in response to two deficit irrigation regimes (50 and 20% ETc) for two cultivars grafted onto the same rootstock, 140 Ruggeri (V. berlandieri x V. rupestris). Root system development was monitored and analyzed using the minirhizotron (MR) system. Two observation tubes (OT) per vine were inserted at two distances from the trunk (DFT), 25 and 75 cm. significant differences were found between scion and irrigation treatment for all root parameters, mainly at depths greater than 1 m. More than 50% of all visible roots were seen between 1.2 and 1.75 m belowground. Root systems of Cabernet Sauvignon (CS) appeared to be more evenly-distributed throughout the soil as compared to Shiraz (SH). Per vine, 56% of CS (0.5) roots were visible in OTs at 25 cm DFT and 44% in OTs at 75 cm DFT, while SH (0.5) was 84% and 16%, respectively. Drought stress resulted in SH root production near the dripper, while no differences were found in CS. Therefore, root structure and size varied greatly between cultivar. This study revealed novel changes in root morphology of the same rootstock grafted on two different grapevine scions.