PURPOSE: Recent emerging evidences suggested that regulatory key transcriptional factors, including myocyte enhancer factor 2C (MEF2C), peroxisome proliferator-activated receptor d(PPARd), and peroxisome proliferator-activated receptorγ coactivator 1a (PGC-1a), are involved in gene expression of glucose transporter 4 protein(GLUT4) and uncoupling protein 3(UCP3), and these factors exert their unique functions in molecular and genetic cascades. METHODS: Present study investigated regulatory effects of exercise training on expression of GLUT4, UCP3, MEF2C, PPARd, and PGC-1a in skeletal muscles (soleus, extensor digitorum logus (EDL)) of obese Zucker rats. After 8 weeks of experiment procedure, oral glucose tolerance test, blood analysis, enzyme activity, analyses of protein and mRNA were performed. RESULTS: Treadmill running exercise significantly improved the insulin sensitivity and increased in citrate synthase activity in soleus of obese Zucker rat. However, both exercise training and genotypically-induced obese condition did not alter the basal levels of gene expression in GLUT4, UCP3, MEF2C, PPARd, and PGC-1a in both muscle fibers. Unlike with gene expressions, protein expressions of these factors were selectively up-regulated or down-regulated by regular exercise training or by obese genotype. The protein expression of PPARd and PGC-1a was significantly higher in both muscles, but GLUT4 and MEF2C protein expression was only higher in soleus of obese genotype compared to lean genotype. Interestingly, UCP3 protein expression was significantly decreased in soleus muscle (but not in EDL). CONCLUSIONS: These findings indicate that adaptation of skeletal muscles to exercise training was occurred by enhancement of not only glucose metabolism (GLUT4 and MEF2C protein expression) but also fatty acid oxidation (PPARd and PGC-1a protein expression). The downregulation of UCP3 protein expression may be associated with decrease of thermogenesis and fatty acid oxidation.