Posttranslational endoproteolysis is essential for the production of biologically active peptides from inactive precursors. Six kexin/substilisin-like endoproteases have been characterized in mammalian species. To understand the complex physiological functions of each convertase within a cellular context it is necessary to comprehensively define its tissue distribution and cohabitation with other members of the family. Previous studies demonstrated the distinct distribution of PC1, PC2, and furin mRNAs in the pituitary and brain, suggesting a unique function for each enzyme. In the present study, the mRNA tissue distributions of the two most recent and homologous members, PC5 and PACE4, were analyzed in rat pituitary and brain using in situ hybridization histochemistry. In the pituitary, the anterior lobe exhibited moderate levels of PC5 and high levels of PACE4 mRNAs. The intermediate lobe showed low levels of PC5 expression, while PACE4 mRNA levels were undetectable. PACE4 transcripts were detected throughout cells of the neural lobe suggesting expression in pituicytes. In the brain, PC5 expression was more restricted than PACE4. PC5 mRNA was detected only in neuronal cells, whereas PACE4 mRNA was expressed in both neuronal and glial cells. In areas that are rich in neuropeptides such as cortex, hippocampus, and hypothalamus, mRNA levels of PC5 were high but PACE4 were low or undetectable. In regions, such as the amygdaloid body and thalamus, distinct but complementary distributions of PC5 and PACE4 mRNAs were observed. The medial habenular and cerebellar Purkinje cells expressed very high levels of PACE4 mRNA. The present data strongly suggest unique tissue-specific functions of PC5 and PACE4.