Skeletal muscle undergoes adaptation following repetitive bouts of exercise. We hypothesize that transcriptional reprogramming and cellular remodeling start in the early phase of long-term training and play an important role in skeletal muscle adaptation. The aim of this study was to define the global mRNA expression in mouse plantaris muscle during (run for 3 and 12 h) and after (3, 6, 12, and 24 h postexercise) a single bout of voluntary running and compare it with that after long-term training (4 wk of running). Among 15,832 gene elements surveyed in a high-density cDNA microarray analysis, 900 showed more than twofold changes at one or more time points. K-means clustering and cumulative hypergeometric probability distribution analyses revealed a significant enrichment of genes involved in defense, cell cycle, cell adhesion and motility, signal transduction, and apoptosis, with induced expression patterns sharing similar patterns with that of peroxisome proliferator activator receptor-gamma coactivator-1alpha and vascular endothelial growth factor A. We focused on the finding of a delayed (at 24 h postexercise) induction of mRNA expression of cell cycle genes origin recognition complex 1, cyclin A2, and cell division 2 homolog A (Schizoccharomyces pombe) and confirmed increased cell proliferation by in vivo 5-bromo-2'-deoxyuridine labeling following voluntary running. X-ray irradiation of the hindlimb significantly diminished exercise-induced 5-bromo-2'-deoxyuridine incorporation. These findings suggest that a single bout of voluntary running activates the transcriptional network and promotes adaptive processes in skeletal muscle, including cell proliferation.