Nitrogen use efficiency (NUE) is an important trait for cereal improvement, but genetically complex. One difficulty in unraveling the genetic control of NUE is that different and sometimes competing physiological processes contribute to improved nitrogen utilization. We have employed a functional genomics approach that integrates field phenotyping, metabolite analysis, and gene expression profiling as a means to discover genes and/or markers that could be used in molecular breeding approaches to improve nitrogen utilization in corn. The agronomic trait most highly correlated with improved N utilization is kernel number, which is sensitive to differences in source N supply. To understand the transcriptional changes associated with kernel number response to N, Illumina RNA Seq was used to monitor steady state RNA levels of developing kernels cultured in vitro with different N treatments. These treatments assessed the physiological states of full N sufficiency, onset of N stress, recovery from N stress, and prolonged N deficiency. These treatments were also surveyed in five hybrid genotypes that differ significantly for their N utilization. Of 39,656 genes deduced and compiled in the most recent maize gene build 5b.60, 17,364 genes were detected to be active in growing kernels. Further, of 7,709 that showed greater than two fold change in their expression in at least one treatment comparison, 5,030 genes showed differential accumulation across all the treatments. A number of genes known to respond to N availability behaved as predicted in the genotypes and N treatments, and additional genes were identified whose expression profiles suggest they may function in either maintaining kernel growth under conditions of limited N supply, or enhancing growth in the presence of sufficient N.