Deficiency of manganese (Mn) is a serious problem reducing crop yields on calcareous and sandy soils throughout the world. In maize, limited knowledge is available on genotypic differences in tolerance to low-Mn supply and the physiological mechanisms underlying this tolerance. In the present study we have evaluated twelve maize genotypes (inbred lines) for their tolerance to Mn deficiency. The evaluation was based on measurements of how low-Mn supply affected shoot biomass, leaf Mn concentrations, maximum quantum efficiency of photosystem II (F_v/F_m), photosynthetic net CO₂ assimilation, root length, Mn uptake and root-shoot Mn translocation. Tolerant genotypes were able to maintain optimum F_v/F_m values under a longer period of Mn deficiency with less reduction of foliar Mn concentration and photosynthetic rate, resulting in less reduction of shoot biomass, compared to sensitive genotypes. Efficient root uptake of Mn and root-to-shoot translocation of Mn also contributed to improved tolerance to Mn-deficiency. The metal transport genes YSL, NRAMP, ZIP, CAX and MTP, involved in root Mn uptake, root-to-shoot Mn translocation and vacuolar Mn homeostasis, were more highly expressed in the efficient genotype K22compared to sensitive genotype BY815. With respect to breeding of maize cultivars with improved Mn-efficiency, the time-course of changes in F_v/F_m values in response to Mn-deficiency provides a useful screening index for low-Mn tolerance.