N is a key macronutrient for plant growth and development. Breeding maize with improved efciency in N use could help reduce environmental contamination as well as increase proftability for the farmers. Quantitative trait loci (QTL) mapping of traits related to N metabolism in the root tissue was undertaken in a maize testcross mapping population grown in hydroponic cultures. N concentration was negatively correlated with root and total dry mass. Neither the enzyme activities nor metabolites were appreciably correlated between the root and leaf tissues. Repeatability measures for most of the enzymes were lower than for dry mass. Weak negative correlations between most of the enzymes and dry mass resulted likely from dilution and suggested the presence of excess of enzyme activities for maximal biomass production. Glutamate synthase and alanine aminotransferase each explained more variation in glutamate concentration than either aspartate aminotransferase or asparagine synthetase whereas glutamine synthetase was inconsequential. Twenty-six QTL were identifed across all traits. QTL models explained 7–43% of the variance with no signifcant epistasis between the QTL. Thirteen candidate genes were identifed underlying QTL within 1-LOD confdence intervals. All the candidate genes were located in trans confguration, unlinked or even on diferent chromosomes, relative to the known genomic positions of the corresponding structural genes. Our results have implications in improving NUE in maize and other crop plants.