Autism Spectrum Disorder (ASD) is a prototypic pervasive developmental disorder characterized by social interaction, and communication deficits, repetitive, stereotypic patterns of behavior, and impairments in language and development. Clinical studies have identified mitochondrial disturbances at the levels of DNA, activity, complexes, oxidative stress, and metabolites in blood and urine of ASD patients. However, these observations from postmortem brains or peripheral tissues do not provide a direct link between autism and mitochondria. The synaptic abnormality of autistic patients has not been investigated yet. Here we review the findings of clinical studies investigating mitochondrial involvement in ASD patients, focusing particularly on the brain and the limitations and future directions needed in order to fully understand the role of mitochondria in ASD pathology.