We have used blood-oxygenation-level-dependent (BOLD) contrast functional magnetic resonance imaging (fMRI) to characterise brain regions responsive to a regulator of appetite. An anorectic dose of the 5-HT(1B/2C) receptor agonist m-chlorophenylpiperazine (mCPP; 3 mg/kg s.c.) was used to compare BOLD contrast fMRI with expression of the c-Fos protein. mCPP was administered to rats, which were then anaesthetised and perfused with fixative 90 min later to allow immunohistochemistry. In a separate experiment, rats were imaged using a T(2)*-weighted gradient echo in a 7 T magnet for 70 min under alpha-chloralose anaesthesia. Both methods detected positive activation in areas of the limbic system: cingulate and orbitofrontal cortices, nucleus accumbens, paraventricular and dorsomedial regions of the hypothalamus. fMRI detected increased signal in the pontine nuclei, the hippocampal formation and olfactory cortex, areas that did not display c-Fos. In addition, BOLD signal was diminished in the ventral tegmental area, preoptic area and the cerebellum-presumably due to decreased neuronal signalling and, therefore, unlikely to display c-Fos. Activity in the limbic system may reflect the appetitive agonist activity of mCPP at the 5-HT(2C) receptor. We conclude that c-Fos provides excellent spatial information but is less useful for detecting inhibited regions, whereas fMRI provides greater temporal resolution. Thus, the two methodologies provide complementary details of brain activity following pharmacological challenge.