Partial rootzone drying (PRD) is an irrigation technique where water is distributed unevenly to the root system such that part is irrigated while the remainder is allowed to dry the soil. Tomato (Lycopersicon esculentum Mill.) plants were grown with their roots in two soil columns to compare the physiological consequences of alternation of wet and dry columns during PRD irrigation (alternate PRD, PRD-A) with retention of the same wet and dry columns (fixed PRD, PRD-F). When PRD plants received 50% less water than well-watered (WW) plants, xylem ABA concentration ([X-ABA]) increased and stomatal conductance decreased relative to WW plants. Although both sets of PRD plants received the same amount of water, [X-ABA] of PRD-A plants increased up to 2-fold above that of PRD-F plants, which further decreased stomatal conductance. Differences in [X-ABA] were detected within an hour of alternation, but did not persist beyond the photoperiod of alternation. [X-ABA] increased linearly as whole-pot soil water content (θpot) and leaf water potential (Ψleaf) declined, but the difference in [X-ABA] between the two sets of PRD plants was not due to differences in either θpot or Ψleaf. In PRD-F plants, the unwatered part of the root system contributes proportionally less to the transpiration stream as the soil progressively dries (Yao et al. 2001, Plant, Cell & Environment 24, 227–235). In PRD-A plants, we hypothesise that re-watering the dry part of the root system allows these roots to contribute proportionally more to total sap flux, thus liberating a pulse of ABA to the transpiration stream as the root ABA pool accumulated during soil drying is depleted. Since the enhancement of [X-ABA] caused by PRD-A increased as θpot and Ψleaf declined, an optimal frequency of alternation to maximise the cumulative physiological effects of this ABA pulse must consider possible negative impacts of leaf water deficit as soil water status declines.