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Abstract: The hypothalamo-neurohypophyseal system (HNS) is a highly specialised region of the brain that is comprised of the magnocellular neurons of the paraventricular (PVN) and supraoptic (SON) nuclei, the axons of which project to the neural lobe of the pituitary. The PVN and the SON are involved in abroad spectrum of activities including, but not restricted to, osmotic regulation, cardiovascular control, parturition and lactation, energy homeostasis and the stress response resulting in a function-related plasticity of these tissues, allowing them the modulation necessary to reply to the physiological demands in an appropriate manner. We hypothesise that the HNS response to physiological stimulation is underpinned by changes in gene transcription. Affymetrix microarrays with 31,099 probes representing the total rat genome, were interrogated with RNA targets from SON, PVN and the neuro-intermediate lobe dissected from naïve rats as well as those responding to physiological and pathological cues. The data generated are comprehensive catalogues of genes that are expressed in each tissue, as well as lists of genes that are differentially regulated following changes in the physiological state of the animal.