We have employed microarray technology using Affymetrix 230 2.0 genome chips, initially to catalogue the transcriptome of the SFO under control conditions, and secondly to evaluate the changes (common and differential) in gene expression induced by the physiological challenges of fluid and food deprivation. We have identified a total of 17,293 genes tagged as present in one of our 3 experimental conditions transcripts which were then used as the basis for further filtering and statistical analysis. In total, the expression of 46 genes was changed in the SFO following dehydration compared to control animals (22 up-regulated, 24 down-regulated), with the largest change being the >5 fold increase in brain derived neurotrophic factor (BDNF) expression, while significant changes in the expression of the calcium sensing (up-regulated), and apelin receptors (down-regulated) were also reported. In contrast food deprivation caused > 2 fold changes in a total of 687 transcripts (222 up-regulated, 465 down-regulated), including significant reductions in vasopressin (VP), oxytocin (OT), pro-melanin concentrating hormone (PMCH), cocaine amphetamine related transcript (CART) and the endothelin B receptor, as well as increases in expression of the GABA-B receptor. Of these regulated transcripts we identified 37 that are commonly regulated by fasting and dehydration, 9 that were uniquely regulated by dehydration and 650 that are uniquely regulated by fasting. We also found 5 transcripts which were differentially regulated by fasting and dehydration including BDNF and CART. In these studies we have for the first time described the transcriptome of the rat SFO, and have in addition identified genes the expression of which is significantly modified by either water or food deprivation.