The anatomy of the graft tissue between a rootstock and its shoot (scion) can provide a mechanistic explanation of the way dwarfing Malus rootstocks reduce shoot growth. Considerable xylem tissue disorganization may result in graft tissue having a low hydraulic conductivity (k(h)), relative to the scion stem. The graft may influence the movement of substances in the xylem such as ions, water and plant-growth-regulating hormones. Measurements were made on 3-year-old apple trees with a low-pressure flow system to determine k(h) of root and scion stem sections incorporating the graft tissue. A range of rootstocks was examined, with different abilities of dwarfing; both ungrafted and grafted with the same scion shoot cultivar. The results showed that the hydraulic conductivity (k(hroot)) of roots from dwarfing rootstocks was lower compared with semi-vigorous rootstocks, at least for the size class of root measured (1.5 mm diameter). Scion hydraulic conductivity (k(hs)) was linked to leaf area and also to the rootstock on to which it was grafted, i.e. hydraulic conductivity was greater for the scion stem on the semi-vigorous rootstock. Expressing conductivities relative to xylem cross-sectional areas (k(s)) did not remove these differences suggesting that there were anatomical changes induced by the rootstock. The calculated hydraulic conductivity of the graft tissue was found to be lower for grafted trees on dwarfing rootstocks compared to invigorating rootstocks. These observations are discussed in relation to the mechanism(s) by which rootstock influences shoot growth in grafted trees.