The effects of food restriction on the serotonergic system were investigated immunohistochemically in both the midbrain and hypothalamic regions of rats. Rats were fed on a restricted feeding schedule consisting of half of the ad libitum quantity for 1, 2, 4 and 6 weeks and a free feeding schedule for 1 week. The optical density of serotonin-positive neurons in the raphe nuclei of the midbrain was found to be significantly lower in the 1 week-food restricted group than in the ad libitum fed control. In the hypothalamus, serotonin-positive neurons were observed in the 1 and 2 week food restricted groups but not in the 4 and 6 week-food restricted groups. This finding was confirmed by immunohistochemistry with tryptophan hydroxylase, a serotonin synthesizing enzyme. In this study, we provide morphological evidence that food restriction has a significant effect on the serotonergic system of the midbrain and hypothalamic regions and suggest some possibilities for the ectopic expression of serotonin-positive neurons after food restriction.