Understanding of muscle adaptation to various stimuli is difficult due to the complex nature of stimuli and responses. In particular, responses to perturbations in energy metabolism require careful examination as they may involve both structural and functional elements. To estimate the structural component of the myocyte adaptation to energetic deficiency, we used transgenic mice with blocked expression of mitochondrial and cytosolic creatine kinases (CK). The ultrastructure was analyzed using the stereological method of vertical sections applied to electron microscopic images of ultrathin longitudinal sections of fast muscle fibers of gastrocnemius, known to adapt to CK deficiency by increasing oxidative metabolism. The lack of creatine kinase induced a profound structural adaptation response that included changes in the volume and surface densities of major organelles. Additionally, using a new stereological parameter - the environment of an organelle - substantial changes in the mitochondrial neighborhood were identified pointing to their relocation closer to the major sites of energy consumption, supposedly to compensate for invalidated energy transfer. Using quantitative arguments we show for the first time that spatial relations among organelles of muscle cells undergo adaptation in response to non-structural stimuli like metabolic deficiency.