Introduction Increases in mitochondrial reactive oxygen species (ROS) and susceptibility to mitochondrial-driven apoptosis are implicated in the decline of muscle mass with aging. However, whether these changes in mitochondrial function explain the differential atrophy between muscles has not been determined. We hypothesized that age-related increases in mitochondrial ROS production and increases in sensitivity of the mitochondrial permeability transition pore (mPTP) to Ca2+ would be greater in muscles with greater degree of atrophy. Methods We prepared permeabilized myofibers from four muscles of young adult and senescent Fisher344/BN rats: 1) mixed gastrocnemius (mGas; fast twitch); 2) extensor digitorum longus (EDL; fast twitch); 3) soleus (Sol; slow twitch); and 4) adductor longus (AL; slow twitch). We measured mitochondrial H2O2 release, Ca2+ retention capacity (CRC) and activity of antioxidant enzymes. Results Muscle mass was significantly lower in SEN than in YA mGas (−38%), EDL (−21%), and SOL (−21%), but was higher in AL (+45%). When expressed per O2 flux, H2O2 release under State 3 respiration was 52% higher with aging only in mGas (mGas > Sol > EDL > AL). Adjusting data for H2O2 scavenging potential of antioxidant enzymes increased theoretical H2O2 release from fast-twitch muscles and decreased that of slow-twitch muscles (mGas > EDL > Sol > AL). Time to mPTP opening was lower only in EDL (−37%) and mGas (−29%), whereas the amount of Ca2+ necessary to trigger opening of the PTP was lower (−19%) only in EDL. Conclusion Mitochondrial H2O2 release was greater in the mGas muscle exhibiting the highest degree of atrophy. However, mPTP sensitivity to Ca2+ was not associated with degree of atrophy. Differences in mitochondrial ROS but not mPTP sensitivity may explain differential atrophy between muscles with aging.