We describe a patient with isolated exercise intolerance caused by a new, maternally inherited mutation in mitochondrial DNA. The heteroplasmic T>C transition at position 13271 in MTND5 affects a highly conserved base and segregates with the disease, being present at highest levels in skeletal muscle fibres showing abnormal mitochondrial accumulation. This is the 15th mutation affecting the MTND5 subunit of respiratory chain complex I and confirms this protein as an important site for disease with phenotypes ranging from MELAS and infantile encephalopathies to isolated syndromes affecting a single tissue such as Leber hereditary optic neuropathy and now skeletal muscle.