The calcium binding proteins parvalbumin and calbindin are thought to differentially regulate physiological functions and often show complementary distributions in the CNS. Our goal was to determine parvalbumin and calbindin distributions in the different subdivisions of mouse auditory thalamus and auditory cortex. Following fixation, FVB mouse brains (postnatal days 38-80) were sectioned along coronal and horizontal planes, then processed for parvalbumin and calbindin immunohistochemistry (antibodies: parvalbumin pa-235, calbindin-d-28k cl-300). Strong complementary differences in calcium binding protein distributions were found in mouse auditory thalamus. The ventral division of the medial geniculate, which is the principal relay to primary auditory cortex, exhibited dense parvalbumin but weak calbindin immunoreactivity. In contrast, most of the 'secondary' auditory thalamic regions surrounding the ventral division showed strong calbindin and lighter parvalbumin levels. Thus, the mouse auditory thalamus is composed of a parvalbumin positive 'core' surrounded by a calbindin positive 'shell'. Parvalbumin immunoreactivity was also more prominent in the primary auditory cortex than in the secondary belt auditory cortex. Calbindin immunoreactivity in auditory cortex was less clearly divided along primary/secondary lines, especially in supragranular layers. However, within infragranular layers, there was heavier staining in belt areas than in primary auditory cortex. In auditory thalamus, parvalbumin labeling was largely confined to the neuropil, whereas calbindin labeling involved somata and neuropil. In auditory cortex, somata and neuropil were positive for both proteins. In summary, the calcium binding proteins parvalbumin and calbindin were found to be differentially distributed within the primary and non-primary regions of mouse auditory forebrain. These differences in protein distribution may contribute to the distinct types of physiological responses that occur in the primary vs. non-primary areas. © 2001 IBRO. Published by Elsevier Science Ltd. All rights reserved.