Even though immobilization of a slow skeletal muscle in a lengthened position prevents muscle atrophy, it is unknown whether this treatment would prevent a decrease in mitochondrial quantity. We found that, regardless of muscle length in immobilized limbs, the mRNA of a marker for mitochondrial quantity, cytochrome c, decreased. Cytochrome c mRNA per milligram of muscle was 62 and 72% less 1 wk after fixation of the soleus muscle in shortened and lengthened positions, respectively, than age-matched controls. Cytochrome c mRNA per milligram wet weight was 36 and 32% less in the tibialis anterior muscle fixed for 1 wk in the shortened and lengthened positions, respectively, compared with age-matched controls. Recently, in the 3'-untranslated region of cytochrome c mRNA a novel RNA-protein interaction that decreases in chronically stimulated rat skeletal muscle was identified. [Z. Yan, S. Salmons, Y. L. Dang, M. T. Hamilton, and F. W. Booth. Am. J. Physiol. 271 (Cell Physiol. 40): C1157-C1166, 1996]. The RNA-protein interaction in the 3'-untranslated region of cytochrome c mRNA in soleus and tibialis anterior muscles was unaffected by fixation in either shortened or lengthened position. We conclude that, whereas lengthening muscle during limb fixation abates the loss of total muscle protein, the percentage decrease in cytochrome c mRNA is proportionally greater than total protein. This suggests that the design of countermeasures to muscle atrophy should include different exercises to maintain total protein and mitochondria.