Crop plant development is strongly dependent on the availability of nitrogen in the soil and the efficiency of nitrogen utilization for biomass production and yield. However, knowledge about molecular responses to nitrogen deprivation derives mainly from the study of model species. In this paper, the metabolic adaptation of source leaves to low N was analyzed in maize seedlings by parallel measurements of transcriptome and metabolome profiling. Inbred lines A188 and B73 were cultivated under sufficient (15mM) or limiting (0.15mN) nitrate supply for up to 30 days. Limited availability of nitrogen caused strong shifts in the metabolite profile of leaves. The transcriptome was less affected by the nitrogen stress but showed strong genotype and age dependent patterns. Nitrogen starvation initiated the selective down-regulation of processes involved in nitrate reduction and amino acid assimilation; ammonium assimilation related transcripts on the other hand were not influenced. Carbon assimilation related transcripts were characterized by high transcriptional coordination and general down-regulation under low nitrogen conditions. Nitrogen deprivation caused a slight accumulation of starch, but also directed increased amounts of carbohydrates into the cell wall and secondary metabolites. The decrease in N availability also resulted in accumulation of phosphate and by strong down-regulation of genes usually involved in phosphate starvation response, underlining the great importance of phosphate homeostasis control under stress conditions.