We have recently shown that CART peptides exhibit a diurnal rhythm in blood that is affected by food intake and glucocorticoids. In the present study, we extend our observations by demonstrating that CART peptides also exhibit a diurnal rhythm in several brain regions, notably the nucleus accumbens, hypothalamus and amygdala, but not in the midbrain. To examine whether the CART peptide rhythm was dependent on food intake, animals were food-deprived for 24 h. In regular-fed animals, CART peptide levels were lower in the morning compared to evening hours. However, this diurnal variation of CART peptide was not apparent in fasted animals, and CART peptide levels were reduced. The diurnal variation of CART mRNA in the nucleus accumbens paralleled the variation of CART peptide in this region. Similar to the peptide, the mRNA did not change in midbrain. These results show that CART peptide levels and gene expression undergo a diurnal variation in some brain regions, and the variation is altered by fasting. These findings suggest a variety of regulatory mechanisms for CART and additional considerations for CART's role in brain.