Secondary cerebral damage after traumatic brain injury (TBI) occurs following processes partly initiated by gene expression alterations. DNA methylation in promoter regions is one of several epigenetic modifications, that affect the regulation of gene expression and which is a part of the pathophysiological pathway following TBI. We have investigated expression and cellular localization of DNA-methyltransferase (Dnmts) enzymes by immunohistochemistry (IHC) and confocal microscopy. Nuclear as well as cytoplasmic Dnmt1 was observed in astrocytes, in contrast to its normal neuronal nuclear localization. Interestingly, double staining with Dnmt1 and nestin showed co-localization in some reactive astrocytes in the nucleus alone, while in others this expression pattern was evident both in the nucleus and cytoplasm, in a brain region specific manner. In normal brains, and contralateral to the injury, the great majority of Dnmt1 positive cells were neurons. We also observed cytoplasmic Dnmt1 in peri-ventricular nestin expressing cells. Our findings may form the basis for further epigenetic studies following TBI and new therapeutic strategies to treat TBI patients.