The amygdala is a key component of emotional processing, whose functions rely on a representation of valence. In animal research, evidence of valence-sensitive neural populations in the amygdala exists. In humans, knowing whether the amygdala encodes valence remains debated. This study explored the involvement of the amygdala in valence encoding, presenting 10 odorants of gradual valence to 20 participants during functional neuroimaging. Representational similarity analyses showed that the similarity structure of explicit pleasantness ratings of smells significantly predicts the similarity structure of the activation patterns in the amygdala, suggesting that an encoding of valence does take place in this structure. Multidimensional scaling indicates that the activation patterns of pleasant and unpleasant smells tend to cluster together, suggesting the involvement of distinct neural populations for the encoding of positive and negative valence. Further studies should explore the functional connectivity of these neural populations to differentiate distinct functional networks to which the amygdala contributes.