The medial division of the medial geniculate (MGM) and the posterior intralaminar nucleus (PIN) are association nuclei of the auditory thalamus. We made tracer injections in these nuclei to evaluate/compare their presynaptic terminal and postsynaptic target features in auditory cortex, amygdala and striatum, at the light and electron microscopic levels. Cortical labeling was concentrated in Layer 1 but in other layers distribution was location-dependent. In cortical areas designated dorsal, primary and ventral (AuD, Au1, AuV) terminals deep to Layer 1 were concentrated in infragranular layers and sparser in the supragranular and middle layers. In ectorhinal cortex (Ect), distributions below Layer 1 changed with concentrations in supragranular and middle layers. In temporal association cortex (TeA) terminal distributions below Layer 1 was intermediate between AuV/1/D and Ect. In amygdala and striatum, terminal concentrations were higher in striatum but not as dense as in cortical Layer 1. Ultrastructurally, presynaptic terminal size was similar in amygdala, striatum or cortex and in all cortical layers. Postsynaptically MGM/PIN terminals everywhere synapsed on spines or small distal dendrites but as a population the postsynaptic structures in cortex were larger than those in the striatum. In addition, primary cortical targets of terminals were larger in primary cortex than in area Ect. Thus, although postsynaptic size may play some role in changes in synaptic influence between areas it appears that terminal size is not a variable used for that purpose. In auditory cortex, cortical subdivisiondependent changes in the terminal distribution between cortical layers may also play a role.