The associative inhibitory control of behaviour is a major component of Pavlovian learning theory, but little is known about its functional neuroanatomy. The associative effects of differential inhibition of conditioned behaviour were investigated by mapping learning-related changes in brain activity of the rat with fluorodeoxyglucose autoradiography. Of interest was how a tone is processed in auditory and extra-auditory systems of the rat brain under similar behavioural, but different associative conditions. Conditioned emotional suppression to drink was used to assess training, and summation tests were used to verify that the tone became an inhibitor of conditioned behaviour. In the Inhibitor group, presentations of a tone stimulus alone were intermixed with presentations of a light stimulus followed by footshock. In the Pseudorandom group, the same numbers of tone, light and footshock presentations were used, but they were presented in a pseudorandom fashion. After training, fluorodeoxyglucose uptake was measured during tone presentations. Behavioural responding to the tone was similar during fluorodeoxyglucose uptake in the two groups, yet associative effects were found in brain activity. In the auditory system, the tone produced reduced fluorodeoxyglucose uptake in major relay nuclei (cochlear nucleus and inferior colliculus) in the Inhibitor group relative to the Pseudorandom group. The tone inhibitor produced similar decreases in the septohippocampal system and the retrosplenial cortex. In contrast, the tone inhibitor produced activity increases in somatosensory and reticulocerebellar systems. The findings provide the first detailed map of neural regions involved in the learned associations controlling differential inhibition of conditioned behaviour.