We examined the effects of 35 and 90d of simulated microgravity with or without resistance-exercise (RE) countermeasures on the content of the general skeletal muscle protein fractions (mixed, sarcoplasmic, myofibrillar) and specific proteins that are critical for muscle function (myosin, actin, collagen). Subjects from two studies, using either unilateral lower limb suspension (ULLS) or bedrest (BR), comprised four separate groups: 35dULLS (N=11), 35dULLS+RE (N=10), 90dBR (N=9), and 90dBR+RE (N=8). RE consisted of 4x7 maximal concentric and eccentric repetitions of the quadriceps femoris muscles that were performed 2-3 times per week. Pre and post muscle biopsies were analyzed from the vastus lateralis of all groups and the soleus of the 35dULLS and 90dBR groups. The general protein fractions and the specific proteins myosin, actin and collagen of the vastus lateralis were unchanged (P>0.05) in both control and countermeasures groups over 35 and 90d, despite large changes in quadriceps femoris muscle volume (35dULLS: -9%; 35dULLS+RE: +8% and 90dBR: -18%; 90dBR+RE: -1%). The soleus demonstrated a decrease in mixed (35d ULLS: -12%, P=0.0001: 90dBR: -12%, P=0.004) and myofibrillar (35dULLS: -12%, P=0.009: 90dBR: -8%, P=0.04) protein, along with large changes in triceps surae muscle volume (35dULLS: -11%; 90dBR: -29%). Despite the loss of quadriceps femoris muscle volume or preservation with resistance-exercise countermeasures during simulated microgravity, the quadriceps femoris muscles are able to maintain the concentrations of the general protein pools and the main contractile and connective tissue elements. Soleus muscle protein composition appears to be disproportionately altered during long duration simulated weightlessness.