BACKGROUND AND PURPOSE: It is unknown whether prolonged training is a safe treatment to alleviate exercise intolerance in patients with mitochondrial DNA (mtDNA) mutations. METHODS: The effect of 3 and 12 months training and 3-12 months deconditioning was studied in four patients carrying different mtDNA mutations. RESULTS: Three-month moderate-intensity training increased oxidative capacity by 23%, which was sustained after 6-12 months of low-intensity training. Training and deconditioning did not induce adverse effects on clinical symptoms, muscle morphology and mtDNA mutation load in muscle. CONCLUSION: Long-term training effectively improves exercise capacity in patients with mitochondrial myopathy, and appears to be safe.