Tolerance to high boron concentration in Brassica rapa was primarily due to low net boron uptake by the roots. However, in the two tolerant genotypes, 39–43% of boron uptake was retained in the tap roots, which limited boron accumulation in the leaves, and also contributed to boron tolerance. In the sensitive genotype, 99% of the increase in boron uptake caused by high soil boron accumulated in the leaves, particularly in the leaf margins. Despite higher transpiration rates, lower net boron uptake occurred in the tolerant genotypes. This result cannot be explained by passive boron uptake alone. Active boron efflux was probably responsible for differences in net boron uptake among tolerant and sensitive genotypes. Boron concentration was much lower in the cell walls than in the cell sap of leaves, indicating that storage of boron in the cell walls was not a tolerance mechanism. Despite high boron concentrations in the leaf symplasm, rates of photosynthesis, transpiration and growth were almost unaffected in the tolerant genotypes. The results demonstrate that boron tolerance in Brassica rapa involves boron exclusion at the root level, boron partitioning away from leaves and, as boron accumulates in leaves despite the first two mechanisms, boron tolerance of the leaf tissue itself.