The OLETF rat is a model of hyperphagic obesity in which the animals retain the desire to run voluntarily. 4-wk-old OLETF rats were provided with running wheels for 16 wks before they were sacrificed 5 hr (WL5), 53 hr (WL53), or 173 hr (WL173) after their wheels were locked. Epididymal fat pad mass, adipocyte volume, and adipocyte number were 58%, 39%, and 47% less, respectively, in WL5 than in sedentary (SED) OLETF not given access to wheels. Contrary to ceasing daily running in Fischer 344 x Brown Norway rats, epididymal fat did not increase during the first 173 hrs of running cessation in the OLETF runners. However, lipid peroxidation levels, as determined by total trans-4-hydroxy-2-nonenal (4-HNE), and 4-HNE normalized to Oil Red O was higher in epitrochlearis muscles of SED compared to WL5, WL53, and WL173. Glutathione S-transferase-4 mRNA levels, an enzyme involved in cellular defense against electrophilic compounds such as 4-HNE, were higher in epitrochlearis muscle of WL53 than in WL173 and SED. In contrast, 4-HNE levels in omental fat were unaltered. Epitrochlearis muscle palmitate oxidation and relative transcript levels for peroxisome proliferator-activated receptor (PPAR) and PPAR coactivator 1 were surprisingly not different between runners and SED. In summary, voluntary running was associated with lower levels of lipid peroxidation in skeletal muscle without significant changes in intramyocellular lipids or in mitochondrial markers in OLETF rats at 20 wks of age. Therefore, even in a genetic animal model of extreme overeating, daily physical activity promotes improved health of skeletal muscle.