1. The effects of chronic muscle use on mitochondrial structure, enzymes and gene expression is reviewed. The role of iron deficiency in modulating this adaptation is discussed. 2. Chronic muscle use and disuse alter mitochondrial composition and affect mitochondrial subpopulations differentially. This has implications for an understanding of organelle assembly. 3. Iron deficiency decreases mitochondrial functional mass within muscle by reducing the level of heme and non-heme iron-containing components. This alters the metabolic response during exercise and results in a reduced endurance performance. 4. Both iron deficiency and chronic muscle use represent contrasting experimental models for the study of mitochondrial function and biogenesis.