Micronutrient malnutrition, often called ‘hidden hunger’, affects over two billion people globally. This is particularly problematic in developing countries where widespread zinc (Zn) deficiency exists as a result of a predominantly plant-based diet. Furthermore, supplemental fertilizers are often unavailable or unaffordable in impoverished regions where soil infertility is common. Delivery of more Zn via food grains is theoretically possible through selective breeding strategies, but severe technical difficulties associated with trace element research have limited research on the underlying genetic components of Zn nutrition.• Genetic dissection of Zn nutrition involved a pre-existing doubled haploid mapping population of barley (Hordeum vulgare). Association of mineral nutrient accumulation traits with regions of the barley genome was determined in two seasons of growth to maturity, using mapmanager qtx and QGene 4.0.• Nine genetic loci segregating in the population associated clearly with measured traits, including five that contributed to grain Zn status. Pooling two-row doubled haploids by selecting the three most favourable alleles increased grain Zn content and concentration by an average of 53 and 75%, respectively.• These results will inform breeding efforts for increased Zn density in the major food grain, wheat (Triticum aestivum), by enabling syntenic marker-assisted selection in conventional breeding programmes.