Mitochondrial encephalomyopathies (MEs) are multisystemic inherited disorders affecting tissues with high energy requirement such as the muscle, retina and central nervous system. Progressive external ophthalmoplegia and myopathy are the most common features in adults, and cognitive impairment is rare. In many neurodegenerative disorders, ERPs have been effectively performed to record cognitive slowing on tasks with different amount of information. To analyze the evidence for possible cognitive slowing, a standard auditory oddball paradigm with a button-press response was applied. Participants were 11 non-demented patients affected by mitochondrial encephalomyopathy and 14 age-matched normal controls. This hypothesis was tested using two tasks of different difficulty (pure tone vs. phonetic stimuli). Reaction time (RT), performance (P) and event-related potentials (ERPs) were measured. RT and P were not significantly different between the groups. Patients showed significantly increased N2 latency and reduced P3 amplitude on both tasks. No difference was found in pure tone and phonetic task conditions. Results were interpreted as electrophysiological signs of cognitive slowing--particularly in relation to stimulus evaluation--irrespective of sensory problems, response selection and cognitive load. These findings suggest that in ME patients, there may be a possible dysfunction of neural mechanisms underlying cognitive events and ERP generation.