A large body of evidence has shown that prolonged paradoxical sleep deprivation (PSD) results in hypothalamic-pituitary-adrenal (HPA) axis activation, and in loss of body weight despite an apparent increase of food intake, reflecting increased energy expenditure. The flowerpot technique for PSD is an efficient paradigm for investigating the relationships among metabolic regulation and stress response. The purpose of the present study was to examine the mechanisms involved in the effects of 96 h of PSD on metabolism regulation, feeding behaviour and stress response by studying corticotrophin-releasing hormone (CRH) and orexin (ORX) immunoreactivity in specific hypothalamic nuclei. Once-daily assessments of body weight, twice-daily measurements of (spillage-corrected) food intake, and once-daily determinations of plasma adrenocorticotropic hormone (ACTH) and corticosterone were made throughout PSD or at corresponding times in control rats (CTL). Immunoreactivity for CRH in the paraventricular nucleus of the hypothalamus and for ORX in the hypothalamic lateral area was evaluated at the end of the experimental period. PSD resulted in increased diurnal, but not nocturnal, food intake, producing no significant changes in global food intake. PSD augmented the immunoreactivity for CRH and plasma ACTH and corticosterone levels, characterizing activation of the HPA axis. PSD also markedly increased the ORX immunoreactivity. The average plasma level of corticosterone correlated negatively with body weight gain throughout PSD. These results indicate that augmented ORX and CRH immunoreactivity in specific hypothalamic nuclei may underlie some of the metabolic changes consistently described in PSD.