The lateral bed nucleus of the stria terminalis (BSTL) is involved in mediating anxiety-related behaviors to sustained aversive stimuli. The BSTL forms part of the central extended amygdala, a continuum composed of the BSTL, the amygdala central nucleus, and cell columns running between the two. The central subdivision (BSTLcn) and the juxtacapsular subdivision (BSTLJ) are two BSTL regions that lie above the anterior commissure, near the ventral striatum. The amygdala, a heterogeneous structure that encodes emotional salience, projects to both the BSTL and ventral striatum. We placed small injections of retrograde tracers into the BSTL, focusing on the BSTLcn and BSTLJ, and analyzed the distribution of labeled cells in amygdala subregions. We compared this to the pattern of labeled cells following injections into the ventral striatum. All retrograde results were confirmed by anterograde studies. We found that the BSTLcn receives stronger amygdala inputs relative to the BSTLJ. Furthermore, the BSTLcn is defined by inputs from the corticoamygdaloid transition area and central nucleus, while the BSTLJ receives inputs mainly from the magnocellular accessory basal and basal nucleus. In the ventral striatum, the dorsomedial shell receives inputs that are similar, but not identical, to inputs to the BSTLcn. In contrast, amygdala projections to the ventral shell/core are similar to projections to the BSTLJ. These findings indicate that the BSTLcn and BSTLJ receive distinct amygdala afferent inputs and that the dorsomedial shell is a transition zone with the BSTLcn, while the ventral shell/core are transition zones with the BSTLJ. J. Comp. J. Comp. Neurol. 521:3191–3216, 2013. © 2013 Wiley Periodicals, Inc.