The amygdala and bed nucleus of the stria terminalis (BNST) are thought to subserve distinct functions with the former mediating rapid fear responses to discrete sensory cues and the latter longer "anxiety-like" states in response to diffuse environmental contingencies. Yet, these structures are reciprocally connected and their projection sites overlap extensively. To shed light on the significance of BNST-amygdala connections, we compared the antidromic response latencies of BNST and central amygdala (CE) neurons to brainstem stimulation. Whereas the frequency distribution of latencies was unimodal in BNST neurons (~10 ms mode), that of CE neurons was bimodal (~10 and ~30 ms modes). However, after stria terminalis (ST) lesions, only short-latency antidromic responses were observed, suggesting that CE axons with long conduction times course through the ST. Compared to the direct route, the ST greatly lengthens the path of CE axons to the brainstem, an apparently disadvantageous arrangement. Since BNST and CE share major excitatory basolateral amygdala (BL) inputs, lengthening the path of CE axons might allow synchronization of BNST and CE impulses to brainstem when activated by BL. To test this, we applied electrical BL stimuli and compared orthodromic response latencies in CE and BNST neurons. The latency difference between CE and BNST neurons to BL stimuli approximated that seen between the antidromic responses of BNST cells and CE neurons with long-conduction times. These results point to a hitherto unsuspected level of temporal coordination between the inputs and outputs of CE and BNST neurons, supporting the idea of shared functions.