The amygdala is essential for classical fear conditioning. According to the current model of auditory fear conditioning, the lateral nucleus is the input station of the amygdala for conditioned auditory stimuli, whereas the central nucleus is the output station for conditioned fear responses. Yet, the lateral nucleus does not project to the central medial nucleus, where most brainstem projections of the amygdala originate. The available evidence suggests that the basal nuclei could transmit information from the lateral to the central medial nucleus. However, interposed between the basolateral complex and the central nucleus are clusters of GABAergic cells, the intercalated neurons, which receive inputs from the lateral and basal nuclei and contribute a massive projection to the central medial nucleus. Because it is impossible to predict the consequences of these connections, we correlated the spontaneous and auditory-evoked activity of multiple simultaneously recorded neurons of the lateral, basal, and central nuclei. The spontaneous activity of lateral and basolateral neurons was positively correlated to that of central lateral cells but negatively correlated to that of central medial neurons. In response to auditory stimuli, the firing probability of lateral and central medial neurons oscillated in phase opposition, initially being excited and inhibited, respectively. In light of previous anatomical findings, we propose that the lateral nucleus exerts two indirect actions on central medial neurons: an excitation via the basal nuclei and an inhibition via intercalated neurons.