Turnip (Brassica rapa L.) plants were grown at adequate (25 μmol L−1) or low (<2.5 μmol L−1) boron (B) supply in nutrient solution for 1 month. The shoot and root dry weight was inhibited by up to 77% and 45%, respectively, in response to low B supply. The results of a retranslocation experiment showed that loaded B in the mature leaves was depleted rapidly during the experimental period and that this B was retranslocated to younger leaves as judged by B depletion from mature leaves simultaneously with the appearance of B in new leaves. Up to 89% of the B content of mature leaves was lost during 4 weeks of growth under B-deficient conditions. In addition, in B-deficient plants, a greater proportion of the total plant B was allocated to young leaves compared with B-sufficient plants; the opposite was observed for old leaves. Chlorophyll and carotenoid concentrations dropped in the leaves of B-deficient plants, but anthocyanins and total free phenolics accumulated under these conditions. Slight changes in the maximum and effective quantum yield of PSII, the efficiency of excitation capture of open PSII reaction centers and the electron transport rate indicated that photosynthesis processes conserved their normal activities and that the thylakoid constituents have not been seriously damaged in B-deprived leaves. A reduction in photochemical quenching as a result of B deficiency was attributed to photoinhibition because of reduced leaf chlorophyll and to an increase in the reducing power of leaves because of lower CO2 assimilation following impaired stomatal conductance. Although the activity of anti-oxidant defense enzymes was elevated under B deficiency, these enzymes did not provide sufficient protection from oxidative damage as judged by the higher accumulation of malondialdehyde (MDA), H2O2 and tissue K+ leakage compared with control plants. Higher accumulation of phenolics and greater activity of polyphenol oxides (PPO) in the roots compared with leaves was observed in B-deficient plants, whereas activity of phenylalanine ammoia lyase (PAL) mainly occurred in leaves. We suggest that elevated production of reactive oxygen species in the roots of B-deficient plants was mainly the consequence of the accumulation of phenolics and the subsequent production of quinones. In leaves, in contrast, an over-reduction of the photosystems is likely to be the responsible factor for oxidative damage.