The effect of early-onset calorie restriction and aging on the accumulation of electron transport system (ETS) abnormalities was studied in rat skeletal muscle. Rectus femoris and vastus lateralis muscle fibers were analyzed for cytochrome c oxidase (COX) and succinate dehydrogenase (SDH) enzyme activities. Fibers displaying COX negative and SDH hyper reactive (COX-/SDH++) phenotype were followed through 1000-2000 micrometers to determine the frequency and length of these abnormalities as well as the physiological impact on fiber structure. Calorie restricted rats had fewer ETS abnormal muscle fibers. The mean length of ETS abnormal regions in ad libitum rat muscle fibers was similar to calorie restricted rat muscles. ETS abnormal fibers from both diet groups exhibited intra-fiber atrophy. A negative correlation between ETS abnormality length and fiber cross-sectional area (CSA) ratio was observed in both ad libitum and calorie- restricted rats. Although calorie restriction reduced the number of ETS abnormalities, it did not affect the length or associated fiber atrophy of ETS abnormal regions once the abnormality was established. Thus, calorie restriction affects the onset but not the progression of electron transport system abnormalities, thereby, limiting a process that ultimately results in fiber breakage and fiber loss.