We have recently published microarray data from the subfornical organ (SFO; [3]) and the area postrema (AP; [1]) that represent catalogues of gene expression from two circumventricular organs (CVO). In these papers, we have identified the populations of ion channels and G protein-coupled receptors (GPCR) that are expressed in the AP and SFO of the male Sprague Dawley rat under basal conditions and established the transcriptional trends that accompany homeostatic challenge in these tissues. Additionally, we have in the AP, compared the spontaneously hypertensive rat (SHR) to the Wistar Kyoto (WKY) rat control. Here, we shift attention from those neural structures that detect physiological challenge onto a structure that is responsive to such challenge; the paraventricular nucleus (PVN), an integrative hypothalamic brain structure that exhibits a wide functional range and a diverse pattern of innervation and termination; a signal integrator in the brain [2]. Sprague Dawley rats (n=25) were either dehydrated for 72-hours (SD-DH) or fasted for 48-hours (SD-F) or left as controls (SD-CT). Spontaneously hypertensive rats (SHR) and Wistar Kyoto (WKY) rat PVN were also taken. Animals were stunned prior to decapitation and the PVN was removed in an RNAse free manner using a dissecting microscope and stored in RNAlater (Ambion) for <1 month before hybridisation onto Affymetrix 230 2.0 microarrays. Initially, catalogues of genes that are flagged as Present in all microarrays from the PVN for SHR [14,835], WKY [15,428], SD-CT [16,144], SD-DH [15,678] and SD-F [16,136] were established. These represent, with a high degree of confidence mRNA populations expressed in the PVN. When combined, this experiment resulted in 18,355 genes that are under investigation in this experiment which are expressed in at least one of these comparisons. Comparison (ANOVA, p<0.05, Benjamini & Hotchberg, Tukey HSD) between these groups reveals 100-genes that are differentially expressed following dehydration and 3007-genes differentially expressed following fasting; this pattern of over-responsiveness to fasting compared to dehydration was noticed in both the SFO and AP data. In the hypertensive brain, 363-genes were differentially regulated. Comparison between the AP, SFO and PVN revels very little overlap in terms of commonly regulated genes for the SD-DH regulated gene lists, and no overlap between the two CVO’s in the SD-F lists but nearly half of all SFO regulated genes in the SD-F list are also regulated in the PVN following fasting. In the hypertensive brain (AP and PVN) nearly half of those genes in either tissue are commonly regulated. We present a comprehensive catalogue of data from the rat PVN and attempt to unravel physiological significance from these large databases using both conventional molecular validation techniques novel mathematical protocols.