Significant efforts have been directed towards the identification of genes differentially regulated through nitric oxide (NO)-dependent processes. These efforts comprise the use of medium- and large-scale transcriptomic analyses including microarray and cDNA-amplification fragment length polymorphism (AFLP) approaches. Numerous putative NO-responsive genes have been identified in plant tissues and cell suspensions with transcript levels altered by artificially released NO, or endogenously produced. Comparative analysis of the data from such transcriptomic analyses in Arabidopsis reveals that a significant part of these genes encode proteins related to plant adaptive responses to biotic and abiotic stresses. Putative common transcription factor-binding sites in the promoter of NO-regulated genes have been defined. The current challenge remains to validate the interpretations deduced from the transcriptomic analyses and to understand the molecular mechanisms underlying the NO-dependent modulation of the genes of interest.