The loss of muscle mass and strength with aging is well characterized, but our knowledge of the molecular mechanisms underlying the development of sarcopenia remains incomplete. Although menopause is often accompanied with first signs of age-associated changes in muscle structure and function, the effects of hormone replacement therapy (HRT) or menopause-related decline in estrogen production in the muscles of postmenopausal women is not well understood. Furthermore the knowledge of the global transcriptional changes that take place in skeletal muscle in relation to estrogen status has thus far been completely lacking. We used a randomized double-blinded study design together with an explorative microarray experiment to characterize possible effects of continuous, combined HRT and estrogen deprivation on the skeletal muscle of fifteen women. Here, we report the differential response of both Gene Ontology-annotated biological processes and some individual genes responding differentially to the use or non-use of HRT. Our results revealed transcription level changes in, for example, muscle protein and energy metabolism. In particular, the ubiquitine-proteosome system was found to be effected at several levels. HRT seemed to partially counteract the postmenopause-related transcriptional changes. Our results suggest that during the early postmenopausal years, when there is no counteracting medication available, muscle transcriptome changes notably, whereas HRT appears to slow down this phenomenon and could therefore aid in maintaining proper muscle mass and function after menopause.