We have examined the transcript distribution of six members of the murine paired box-containing gene family (Pax-gene family) in midgestation embryo and adult brain using in situ hybridization analysis. The expression domains of several Pax-genes in the embryo brain were found to correspond with anatomical boundaries that coincide with neuromere landmarks and therefore respect former neuromere territories in the forebrain. The results are consistent with the concept of brain segmentation and suggest a role for Pax-genes in the brain regionalization. In the adult brain the expression of Pax-genes was observed in discreet areas, with a caudal to rostral restriction in the number of the expressed genes. In general the distribution of transcripts along the anterior-posterior axis was similar to that found in midgestation embryo brain, suggesting a role for Pax-genes in the commitment of the precursor cells to different neuronal cell fates and in the maintenance of specific brain cell subtypes. In the cerebellar cortex, the granular cell layer was found to express high levels of the Pax-6 gene, while putative Bergmann glia and cells surrounding the Purkinje cells contained Pax-3 transcripts. The main adult brain structures that expressed distinct Pax-mRNAs were the periglomerular and granular cell layer of olfactory bulb, nuclei of the septum, amygdala, and isthmus, which suggests a role for the Pax-gene family in the specification of the subcortical domains of the evolutionary old limbic system.