Rett Syndrome (RTT) is a neurological X–linked dominant disorder, characterized by the arrest of normal development, cognitive and social regression, loss of speech, and repetitive hand movements. At the cellular level, neurons are densely packed, showing reductions in length, complexity and number of dendritic spines. This disorder affects 1 in 10,000 girls world-wide, and in ~95% of the cases is caused by mutations in the Methyl-CpG-binding protein 2 (MeCP2). Although the genetic component of the disease was identified, the cellular pathways and neuronal functions contributing to the etiology of RTT are still elusive. MeCP2 binds and regulates genomic sequences with methylated cytosines, which form the most basic layer of the epigenome called DNA methylation. Here, we have performed whole-genome bisulfite-sequencing of hippocampal neurons from a RTT mouse model to investigate perturbation of normal DNA methylation patterns at single base-pair resolution.Thishigh-resolutiondetection of DNA methylation differences has allowed the identification of potential MeCP2 targets and candidate regulatory elements that are differentially activated in RTT and control samples. The genes and pathways identified in this work provide a better understanding of the genomic dysregulation that takes place in RTT at the molecular level, with the potential toinform future development of therapeutic approaches for this disorder.