The effects of classical fear conditioning in different regions of the limbic system were analysed using cytochrome oxidase (CO) histochemistry. Wistar rats were submitted to different conditions. Rats in the group Paired received tone-shock pairing, to elicit conditioned suppression of lever pressing (i.e., tone will evoke conditioned fear responses). The group Unpaired underwent random presentations of these stimuli and developed no conditioned fear. Untrained animals were also included as a control group. A significant decrease in CO activity was found in the medial septal area and the dorsal hippocampus (CA3 subfield and dentate gyrus) in the group Paired as compared with the group Unpaired. Furthermore there was greater metabolic activity in the control group as compared with the other two groups. No differences in CO labelling of the basolateral amygdala were detected among all groups. These findings suggest that the septohippocampal system plays an important role in controlling conditioned fear behaviour.