Conduct Disorder (CD) is an impairing psychiatric disorder of childhood and adolescence characterized by aggressive and dissocial behavior. Environmental factors such as maternal smoking during pregnancy, socio-economic status, trauma, or early life stress are associated with CD. We performed a genome-wide methylation sequencing of 49 CD girls and 50 matched typically developing controls. We identified a 12% increased methylation 5’ of the neurite modulator SLITRK5 (FDR = 0.0046) in cases within a glucocorticoid receptor binding site. Functionally, methylation positively correlated with gene expression in lymphoblastoid cell lines. In addition, we found the epigenetic signatures of a gene network activated in the thalamus during early childhood correlated with the effect of parental education on CD status possibly mediating its protective effect.