In the brain, domoic acid especially damages the hippocampus and amygdaloid nucleus.

The posterior insula projects predominantly to the dorsal aspect of the lateral and to the central amygdaloid nuclei.

The plaques occur commonly in the amygdaloid nucleus and the sulci of the cortex of brain.

The gray matter of the caudate nucleus bends upon itself, and its other end is the amygdaloid nucleus ("almond-shaped," again because of its shape).

In human PET studies WAY-100,635 shows high binding in the cerebral cortex, hippocampus, raphe nucleus and amygdaloid nucleus, while lower in thalamus and basal ganglia.

In contrast, the anterior insula projects to the anterior amygdaloid area as well as the medial, the cortical, the accessory basal magnocellular, the medial basal and the lateral amygdaloid nuclei.

First it is considered to be part of the basal forebrain, the nucleus accumbens, and the amygdaloid nuclei because of its location along the rostral ventral region of the brain; that is the front bottom part.