In order to thrive, animals must be able to recognize aversive and appetitive stimuli within the environment and subsequently initiate appropriate behavioral responses. This assignment of positive or negative valence to a stimulus is a key feature of emotional processing, the neural substrates of which have been a topic of study for several decades. Until recently, the result of this work has been the identification of specific brain regions, such as the basolateral amygdala (BLA) and nucleus accumbens (NAc), as important to valence encoding. The advent of modern tools in neuroscience has allowed further dissection of these regions to identify specific populations of neurons signaling the valence of environmental stimuli. In this review, we focus upon recent work examining the mechanisms of valence encoding, and provide a model for the systematic investigation of valence within anatomically-, genetically-, and functionally defined populations of neurons.