Certain sounds, for example, the squeal of chalk on a blackboard, are perceived as highly unpleasant. Functional magnetic resonance imaging (fMRI) in humans shows responses in the amygdala and auditory cortex to aversive sounds. Dynamic causal modelling (DCM) of the interaction between auditory cortex and the amygdala revealed that evoked responses to aversive sounds are relayed to the amygdala via the auditory cortex. There is a complex interaction between the auditory cortex and amygdala involving effective connectivity in both directions. While acoustic features modulate forward connections from auditory cortex to the amygdala, the valence modulates effective connectivity from the amygdala to the auditory cortex. The results support interaction between the auditory cortex and amygdala where stimuli are first processed to a higher (object) level in the auditory cortex before assignment of valence in the amygdala.