Zinc (Zn) deficiency is a widespread problem which reduces yield and grain nutritive value in many cereal growing regions of the world. While there is considerable genetic variation in tolerance to Zn deficiency (also known as Zn efficiency), phenotypic selection is difficult and would benefit from the development of molecular markers. A doubled haploid population derived from a cross between the Zn inefficient genotype RAC875-2 and the moderately efficient genotype Cascades was screened in three experiments to identify QTL linked to growth under low Zn and with the concentrations of Zn and iron (Fe) in leaf tissue and in the grain. Two experiments were conducted under controlled conditions while the third examined the response to Zn in the field. QTL were identified using an improved method of analysis, whole genome average interval mapping. Shoot biomass and shoot Zn and Fe concentrations showed significant negative correlations, while there were significant genetic correlations between grain Zn and Fe concentrations. Shoot biomass, tissue and grain Zn concentrations were controlled by a number of genes, many with a minor effect. Depending on the traits and the site, the QTL accounted for 12-81% of the genetic variation. Most of the QTL linked to seedling growth under Zn deficiency and to Zn and Fe concentrations were associated with height genes with greater seedling biomass associated with lower Zn and Fe concentrations. Four QTL for grain Zn concentration and a single QTL for grain Fe concentration were also identified. A cluster of adjacent QTL related to the severity of symptoms of Zn deficiency, shoot Zn concentration and kernel weight was found on chromosome 4A and a cluster of QTL associated with shoot and grain Fe concentrations and kernel weight was found on chromosome 3D. These two regions appear promising areas for further work to develop markers for enhanced growth under low Zn and for Zn and Fe uptake. Although there was no significant difference between the parents, the grain Zn concentration ranged from 29 to 43 mg kg(-1) within the population and four QTL associated with grain Zn concentration were identified. These were located on chromosomes 3D, 4B, 6B and 7A and they described 92% of the genetic variation. Each QTL had a relatively small effect on grain Zn concentration but combining the four high Zn alleles increased the grain Zn by 23%. While this illustrates the potential for pyramiding genes to improve grain Zn, breeding for increased grain Zn concentration requires identification of individual QTL with large effects, which in turn requires construction and testing of new mapping populations in the future.