Single unit activity was recorded from the lateral and medial septum of rats during aversive Pavlovian differential conditioning. One conditioned stimulus (CS+) was consistently paired with and another (CS-) was explicitly unpaired with a brief shock unconditioned stimulus (US). In the lateral septum single unit activity generally increased in the presence of a conditioned inhibitor of fear (CS-), while unit activity generally decreased in the presence of a conditioned excitor of fear (CS+). Responses in the medial septum were more heterogeneous. Many cells did not show plastic changes to the CSs, others showed responses to the conditioned stimuli opposite to that seen in the lateral septum. A small group of cells showed responses similar to that seen in the lateral septum. Finally, theta bursting cells were seen in the medial septum with some evidence of increased theta activity in the presence of a conditioned inhibitor of fear (CS-). The results were interpreted as consistent with the proposition that the lateral septum mediates the inhibition of aversive emotional states. The medial septum may have some involvement with the activation of fear or anxiety.