When grown on soils with low micronutrient availability due to either chemical or biological fixation, or spatial or temporal unavailability, micronutrient-efficient genotypes have a greater yield in comparison to inefficient ones, even when fertilized with smaller amounts of fertilizers or less frequently. This review summarizes published information on genotypic differences in Zn, Fe and Mn efficiency. Generally, micronutrient-efficient genotypes are capable of increasing available soil micronutrient pools through changing chemical and microbiological properties of the rhizosphere as well as by growing thinner and longer roots and having more efficient uptake and transport systems. For Zn-efficient genotypes, more efficient utilization of Zn in tissue also contributes to overall Zn efficiency. Understanding micronutrient efficiency mechanisms is important for designing suitable screening techniques for breeding micronutrient-efficient genotypes. Growing micronutrient-efficient genotypes contributes to environmentally-benign agriculture by lowering the input of chemicals and energy. These genotypes also offer a potential for producing grain for human consumption with higher concentration of Fe, Zn and Cu, the three micronutrients that about a third of the world population is deficient in.