Circadian clock genes are rhythmically expressed in many areas of the brain and body and are thought to underlie most endogenous circadian behaviors and physiological processes. Daily rhythms of clock gene expression throughout the brain and body are normally coordinated by the suprachiasmatic nucleus (SCN), but they are also strongly influenced by daily temporal restrictions of food availability. Here, we studied the effects of a daily restricted presentation of highly palatable complete meal replacement, chocolate Ensure Plus (Ensure) in food-deprived (restricted feeding, RF) and free-fed (restricted treat, RT) rats, on the expression of the clock protein, Period2 (PER2) in regions of the brain involved in motivational and emotional regulation; these include the oval nucleus of the bed nucleus of the stria terminalis (BNSTov), the central nucleus of the amygdala (CEA), the basolateral amygdala (BLA), the dentate gyrus (DG) and the dorsomedial hypothalamus (DMH). RF and RT rats consumed similar amounts of Ensure, but changes in the pattern of PER2 expression were seen only in the RF condition, suggesting that changes in PER2 expression in these regions are triggered by the daily alleviation of a negative metabolic state associated with RF and are independent of the positive incentive properties of the consumed substance, per se. In contrast, the expression of the immediate early gene, Fos, was increased in these regions by both RF and RT schedules, showing that signals concerning the incentive value of the consumed food reach these regions. No changes in either PER2 or Fos expression were observed in the SCN of RF or RT rats. These findings demonstrate that mechanisms leading to changes in the expression of PER2 and those affecting the induction of Fos under RF and RT are, at least in part, dissociable.