This study investigated how dietary fat affects muscle atrophy and lipid metabolism in various muscles during hindlimb immobilization in rats. Twenty-four male Sprague?Dawley rats had their left hindlimb immobilized and were divided into four groups by dietary fat content and composition. The contralateral hindlimb (control) was compared with the immobilized limb in all dietary groups. Rats (n = 6/group) were fed a 4% corn oil diet (CO), 2.6% corn oil + 1.4% fish oil diet (FO), 30% corn oil diet (HCO), or a 30% beef tallow diet (HBT)after their hind limbs were immobilized for 10 days. Data were collected for the gastrocnemius, plantaris and soleus muscles. Muscle atrophy was induced significantly after 10 days of hindlimb immobilization, resulting in significantly decreased muscle mass and total muscle protein content. The protein levels of peroxisome proliferator activated receptor (PPAR) in the plantaris, gastrocnemius, and soleus increased following hindlimb immobilization irrespective of dietary fat intake. Interestingly, the PPAR mRNA level in the plantaris decreased significantly in all groups and that in the FO group was lower than that in the other groups. The soleus PPAR mRNA level decreased significantly following hindlimb immobilization in the FO group only. Muscle carnitine palmitoyl transferase 1 (mCPT1) mRNA level was not affected by hindlimb immobilization. However, the mCPT1 mRNA level in the FO group was significantly lower in the plantaris but higher in the soleus than that in the other groups. The pyruvate dehydrogenase kinase 4 (PDK4) mRNA level in the plantaris decreased significantly, whereas that in the soleus increased significantly following hindlimb immobilization. The plantaris, but not soleus, PDK4 mRNA level was significantly higher in the FO group than that in the CO group. The increased PPAR protein level following hindlimb immobilization may have suppressed triglyceride accumulation in muscles and different types of dietary fat may have differentially affected muscle atrophy according to muscle type. Our results suggest that -3 polyunsaturated fatty acids may suppress muscle atrophy and lipid accumulation by positively affecting the expression level and activity of PPAR and PPAR-related enzymes, which are supposed to play an important role in muscle lipid metabolism.