Peroxisome proliferator-activated receptors (PPAR) exist in three different forms, alpha (α), beta/delta (β/δ), or gamma (γ), all of which are expressed in skeletal muscle and play a critical role in the regulation of oxidative metabolism. The purpose of this investigation was to determine the mRNA expression pattern of the different PPARs and peroxisome proliferator-activated receptor alpha coactivator-1 alpha (PGC-1α) in muscles that largely rely on either glycolytic (plantaris) or oxidative (soleus) metabolism. Further, we also examined the alterations in the PPARs mRNA expression after one bout of endurance exercise or after 12 weeks of exercise training in the different muscles. Female Sprague-Dawley rats (5–8 months) were either run on the treadmill once or exercised trained for 12 weeks. The muscles were removed 24 h after the last bout of exercise. The results demonstrated with the exception of PPAR β/δ, the PPAR mRNAs are expressed to a greater extent in the soleus muscle than in the plantaris muscle in sedentary animals. PPARγ was the least abundantly expressed PPAR in either the soleus or the plantaris muscle. With respect to exercise training, only PPARγ mRNA expression increased in the soleus muscle, while PPARβ/δ and γ mRNA levels increased in the plantaris muscle. Minimal changes were detected in any of the PPARs with one bout of exercise training. These results suggest that PPARγ mRNA levels are the lowest in skeletal muscle among all of the PPARs and PPARγ mRNA is the most responsive to changes in physical activity levels.