Protease nexin-1(PN-1) is a potent thrombin inhibitor that is identical to the glia-derived neurite promoting factor or glia-derived nexin. It also plays a role in regulating proteolytic activity of plasminogen activator(PA) system. PN-1 is known to be involved in tissue remodeling, cellular invasiveness, matrix degradation and tumor growth. The multifunctional mammalian N-methylpurine-DNA glycosylase(MPG) is responsible for the DNA repair of alkylating damages. In this study, we examined regional differences of PN-1 and MPG transcript in the adult rat brain. Results show a widespread but heterogeneous patterns of expression. These analyses revealed distinct spatial PN-1 and MPG expression patterns in thalamus, olfactory bulb, midbrain, cerebellum, hippocampus, basal ganglia, septal area, spinal cord, pons, cerebral cortex, pituitary gland and medulla oblongata. Interestingly, PN-1 and MPG expressions were found in all tested brain regions with about two-fold differences(p>0.05). The differential regulation of PN-1 and MPG expression across different regions of the rat brain suggests multiple roles in tissue homeostasis and DNA damages.