The identity and distribution of neurons that are involved in any learning or memory event is not known. In previous studies, we identified a discrete population of neurons in the lateral amygdala that show learning-specific activation of a c-fos-regulated transgene following context fear conditioning. Here, we have extended these studies to look throughout the amygdala for learning-specific activation. We identified two further neuronal populations, in the amygdalo-striatal transition area and medial amygdala, that show learning-specific activation. We also identified a population of hypothalamic neurons that show strong learning-specific activation. In addition, we asked whether these neurons are activated following recall of fear-conditioning memory. None of the populations of neurons we identified showed significant memory-recallrelated activation. These findings suggest that a series of discrete populations of neurons are involved in fear learning in amygdala and hypothalamus. The lack of reactivation during memory recall suggests that these neurons either do not undergo substantial change following recall, or that c-fos is not involved in any such activation and change.Pavlovian fear conditioning is one of the best-characterized models for the study of learning and memory and its neural correlates. It involves the association of a neutral stimulus, the conditioned stimulus (CS) such as a sound or context, with an aversive unconditioned stimulus (US) such as a footshock. Fear conditioning is quite robust, and a large percentage of trained animals show fear learning. It can be examined with respect to several excellent nonlearning controls. Some of the major areas of the brain that are necessary for expression of fear conditioning have been determined by lesioning experiments, with the amygdala playing a central role in the process (Pitkanen et al. 1997;LeDoux 2000;Sah et al. 2003;Fanselow and Poulos 2005;Ehrlich et al. 2009).A large body of evidence implicates the lateral amygdala in the formation and storage of fear memories in the amygdala (LeDoux 1993;Fanselow and LeDoux 1999;Maren and Quirk 2004;Pare et al. 2004;Rodrigues et al. 2004); however, this region does not act in isolation. Anterograde and retrograde tracing studies have yielded a plethora of amygdalar efferents and afferents. The amygdala itself is comprised of several heavily interconnected nuclei and receives a massive array of both cortical (McDonald 1998) and subcortical inputs (Pitkanen et al. 1997;Sah et al. 2003). The amygdala also receives modulatory monoaminergic input from hypothalamic nuclei (Asan et al. 2005); however, this remains poorly characterized.In moving beyond basic functional neuroanatomy, progress in our understanding of the brain requires not only a comprehension of the mechanisms of plasticity, but also of the localized circuitry involved in specific behaviors. Our previous development of the transgenic fos-tau-lacZ (FTL) mouse (Wilson et al. 2002;Murphy et al. 2007) has emerged as an excellent tool for visualizing fun...