Valence of emotion (i.e., the intrinsic attractiveness or aversiveness of an event, object, or situation) is essential to choose between two main behavioral strategies, approach or withdrawal. Many of these behaviors can be modified by experience. The amygdala is a key component of the brain emotional system; however, an understanding of how various emotions are differentially processed in the amygdala has yet to be achieved.We report that matrix metalloproteinase-9 (MMP-9, extracellularly operating enzyme) in the central nucleus of the amygdala (CeA) is crucial for appetitive, but not for aversive, learning in mice. The knock-out of MMP-9 impairs appetitively motivated conditioning, but not an aversive one. Similarly, blocking extracellular MMP-9 activity with its inhibitor TIMP-1 provides evidence that local MMP-9 activity in the CeA is crucial for the appetitive, but not for aversive, learning. Our data challenge the notion of similar molecular mechanisms within the amygdala that govern appetitive and aversive learning, both at the structural and molecular levels.