Recent evidence suggests aerobic exercise may help preserve soleus muscle mass during unloading. The purpose of this investigation was to examine the muscle-specific metabolic response to running as it relates to muscle growth. Mixed-muscle protein synthesis [fractional synthetic rate (FSR)] and gene expression (GE) were examined in the vastus lateralis (VL) and soleus (SOL) muscles from eight men (26 +/- 2 yr; Vo(2max) 63 +/- 2 ml.kg(-1).min(-1)) before and after a 45-min level-grade treadmill run at 77 +/- 1% intensity. Muscle glycogen utilization was similar between muscles. Resting FSR was similar between the VL (0.080 +/- 0.007 %/h) and SOL (0.086 +/- 0.008 %/h) and was higher (P < 0.05) 24 h postexercise compared with rest for both muscles. The absolute change in FSR was not different between muscles (0.030 +/- 0.007 vs. 0.037 +/- 0.012 %/h for VL and SOL). At baseline, myostatin GE was approximately twofold higher (P < 0.05) in SOL compared with VL, while no other muscle-specific differences in GE were present. After running, myostatin GE was suppressed (P < 0.05) in both muscles at 4 h and was higher (P < 0.05) than baseline at 24 h for VL only. Muscle regulatory factor 4 mRNA was elevated (P < 0.05) at 4 h in both SOL and VL; MyoD and peroxisome-proliferator-activated receptor-gamma coactivator-1alpha (PGC-1alpha) were higher (P < 0.05) at 4 h, and forkhead box [FOXO]3A was higher at 24 h in SOL only, while muscle-RING-finger protein-1 (MuRF-1) was higher (P < 0.05) at 4 h in VL only. Myogenin and atrogin-1 GE were unaltered. The similar increases between muscles in FSR support running as part of the exercise countermeasure to preserve soleus mass during unloading. The subtle differences in GE suggest a potential mechanism for muscle-specific adaptations to chronic run training.