Aims We wished to demonstrate the feasibility of performing diagnostic mitochondrial DNA (mtDNA) analysis on biopsies of the orbicularis oculi muscle in patients with a chronic progressive external ophthalmoplegia (CPEO) phenotype and suspicion of an underlying mitochondrial disorder. Method Case series of three patients who underwent ptosis surgery and had simultaneous biopsy of the orbicularis oculi muscle because of a suspicion of a mitochondrial disorder. Orbicularis muscle samples were divided into two pieces at the time of biopsy. The first was snap-frozen in liquid nitrogen, DNA was extracted and mtDNA deletion analysis was performed by two complementary methods (long PCR and Southern blot analysis). The second piece of muscle was assessed using routine histopathology, Results Three patients with clinical features of CPEO, without any positive family history, underwent orbicularis muscle biopsies at time of eyelid ptosis surgery. All biopsies were adequate to conduct histopathological and immuno-histochemical analysis, which showed evidence of abnormal muscle structure and function. mtDNA was successfully extracted from all biopsies, and long PCR and Southern blot analysis confirmed diagnostic large single mtDNA deletions in all three cases. Conclusions Orbicularis oculi muscle biopsies are useful in patients with CPEO to perform mtDNA analysis, thus avoiding a separate biopsy of skeletal muscle elsewhere.