Boron (B) is an essential trace element for higher plants yet it becomes toxic when present at high concentrations. The site of B toxicity in plant roots is located in the root tip, and B tolerance is associated with the concentration of reducing sugars (RS) in this region. In the study reported here, we aimed to detect and map loci associated with this trait using a barley doubled-haploid population derived from a cross between Clipper (B sensitive) and Sahara 3771 (B tolerant). The population was screened at high B supply using solution culture, with the RS concentration measured in the root tip. The RS concentration varied widely in the parents and DH lines, ranging from 14 to 141 mg g-1. Using a linkage map of 420 molecular markers, quantitative trait loci (QTL) were detected on chromosomes 2H, 3H, 5H and 6H. Of these, the QTL on 2H had the largest effect, explaining 16% of the phenotypic variance, with the (high RS) allele contributed from Sahara 3771. QTLs detected here were co-located with reported loci for other B tolerance traits, including leaf symptom, relative root elongation and B uptake, indicating a role of RS in physiological pathways associated with B tolerance.