The present study investigated whether different grafting combinations (hypobiont-epibiont) of Vitis spp. influence root infection with phylloxera and thus vine biomass on potted 2-year-old plants. The study was conducted simultaneously at two locations in Slovenia (VEM) and Hungary (GF). The dormant canes of ‘Johanniter’ (JOH), ‘Riesling’ (RR) and Vitis berlandieri × Vitis riparia ‘Teleki 5C’ (5C) were hetero-grafted (each with each) and autografted (each with itself), so that nine plant combinations were used for the trial. The roots of the experimental plants at different ages (1–2 years) were infested with two phylloxera populations originating from two locations (VEM, GF). Plant growth was quantified 120 days after inoculation by measuring root and shoot biomass, while the extent of phylloxera infestation was assessed by the number of feeding sites (nodosities, tuberosities) and the number of larval stages of phylloxera. In most cases, the genotype of the hypobiont influenced the degree of phylloxera infestation on all roots of the two-year-old root system. At both locations, the highest number of nodosities and the highest increase in phylloxera population was observed on the autografted Teleki 5C (5C/5C). The phylloxera biotype derived from Vitis vinifera roots (GF) induced tuberosities, especially on roots of combinations where JOH and RR were used as hypobionts. No correlation was found between biomass and phylloxera infestation. The hypobiont genotype had no effect on cane biomass at the end of the growth cycle at either experimental site.