Glutamate and gamma-aminobutyric acid (GABA) release in the amygdala are thought to be crucial for the acquisition and expression of fear memories, but the time course of amino acid changes during conditioning is unknown. We used rapid-sampling microdialysis with 14 s temporal resolution to address this issue. During auditory fear conditioning, large, rapid and transient increases in glutamate and GABA were detected, but only during the first noise-shock pairing. In contrast, rats receiving unsignaled shocks during contextual fear conditioning showed no changes in GABA and less glutamate release for the initial shock, but increased glutamate release during later shocks. Expression of conditioned fear to either a white noise or the context previously paired with shock produced similar rapid and transient increases in many amino acids in the amygdala. These experiments demonstrate glutamate and GABA levels in the amygdala are differentially modulated during auditory and contextual fear learning, and are transiently increased during the expression of fear memories.