The loss of estrogen during menopause causes changes in the female body with wide-range effects on health. Estrogen-containing hormone replacement therapy (HRT) leads to a relief of typical menopausal symptoms, benefits bone and muscle health, and associates with tissue-specific gene expression profiles. As gene expression is controlled by epigenetic factors (including DNA methylation) many of which are environmentally sensitive, it is plausible that at least part of the HRT-associated gene expression is due to changes in DNA methylation profile.We investigated genome-wide DNA methylation and gene expression patterns of white blood cells (WBCs) and their associations with body composition, including muscle and bone measures of monozygotic female twin pairs discordant for HRT. We identified 7855 differentially methylated regions (DMRs) associated with 4044 genes. Of the genes with DMRs, five (ACBA1, CCL5, FASLG, PPP2R2B and UHRF1) were al so differenti ally expressed. All have been previously associated with HRT or estrogenic regulation, but not with HRT-associated DNA methylation. All five genes were associated with bone mineral content, and ABCA1, FASLG and UHRF1 were also associated with body adiposity.