Social isolation and loneliness increase the risk of death as much as well-established risk factors for mortality such as cigarette smoking and alcohol consumption. The underlying molecular mechanisms are poorly understood. In the present study, 3 months old male C57BL/6 mice were socially isolated by individual housing for another 3 months. At the age of 6 months, epigenetic changes were analyzed in midbrain. Social isolation of male adult mice led to an increased global DNA methylation, which was associated with enhanced activity of DNA methyltransferase. Di- and trimethylation of global histone H3 lysine 4 (H3K4) were increased in midbrain of socially isolated mice, accompanied by enhanced H3K4 histone methyltransferase activity. In addition, social isolation of adult mice led to activation of histone acetyltransferases as well as of histone deacetylases (HDAC) resulting in a net enhancement of histone H3 lysine 9 (H3K9) acetylation. Gene-specific effects were observed for Hdac1, Hdac3 and the serotonin transporter Slc6a4. Social isolation led to an up-regulation of Hdac1 and Hdac3, associated with decreased DNA methylation in the CpG island of the respective genes. On the contrary, the Slc6a4 gene was down-regulated, which was associated with enhanced DNA methylation. Collectively, the results from the present study demonstrate for the first time that social isolation of adult mice leads to a wide range of global epigenetic changes and these effects may have profound impact on gene expression pattern and phenotype of the socially isolated animals.