Bed Rest (BR), which is the most used human model of microgravity, causes disuse muscle atrophy. Ten healthy sedentary young subjects were subjected to 35-days BR and needle biopsy samples of vastus lateralis were collected pre-BR, post-7-days and post-35-days BR. At 35 days, but not at 7 days of BR, we found a decrease in fiber size and in myosin content and a shift towards MHC-2X myosin isoform. A general down-regulation of myofibrillar proteins, metabolic enzymes and antioxidant defence systems both at 7 and 35 days BR was found by proteomic analysis suggesting a possible role of oxidative stress and metabolic impairment in triggering muscle atrophy. To better investigate their role, we performed RT-PCR and Western Blot analyses. We studied controllers of antioxidant defense systems (Nrf2), oxidative and lipid metabolism (PGC1?, SREBP), and intracellular signaling pathways involved in protein turnover (ubiquitin-proteasome and AKT/mTor) and in autophagy (Beclin1, P62). At 35-days BR the protein degradation system was not activated, the protein synthesis signaling was not depressed whereas the autophagy system was activated. Antioxidant response and oxidative metabolism were up and down-regulated respectively. Lipid synthesis was increased suggesting a resulting lipid accumulation that could determine mitochondrial damage and insulin resistance which in turn could generate oxidative stress and trigger muscle atrophy.