This study measured in vivo synthesis of total RNA and protein from cortex, cerebellum and midbrain/brainstem and 6 major organs from Syrian hamsters (Mesocricetus auratus) during (a) 33 h of torpor (body temperature 5–6°C); (b) 90 min of the early arousal; (c) 90 min of the middle arousal; (d) 90 min in cold adapted cenothermic (CEN) hamsters of the same circannual period. Appropriate physiological parameters were used to confirm the phase of the hibernation cycle during infusion and incorporation of [³H]-uridine and [¹⁴C]-leucine. In torpor, RNA synthesis was 5–25% of CEN levels depending upon tissue. In brain and heart mRNA was not preferentially synthesized. Protein was synthesized at low, tissue specific levels during torpor. Initiation of arousal and the warming of anterior organs via non-shivering thermogenesis during the early arousal occurred without measurable synthesis of RNA or proteins. Tissue specific levels of RNA and protein synthesis occurred later after shivering thermogenesis had been recruited and was strongly influenced by thermal gradients in the body. In the middle arousal phase, protein synthesis is most active in the brain despite modest synthesis of RNA and mRNA. The majority of molecular processing required for the induction and maintenance of torpor and the arousal from torpor up until the onset of shivering thermogenesis occurs during the cenothermic period before the hamster initiates the hibernation cycle.