SUMMARY Introduction. Some kind of migraine has been prove the existence of cortical hyperexcitability and abnormal brain energy metabolism probably due to mitochondrial dysfunction. In these patients is high suspicion of mutations in mitochondrial DNA that are implicated as pathophysiologic mechanisms in this entity. Objective. To identify the A3243G mutation of mitochondrial DNA in patients with complications of migraine, sporadic hemiplegic migraine, basilar type migraine, retinal migraine. Materials and Methods. . A prospective descriptive study of a series of neurological patients in an outpatient of the city of Medellin, with a diagnosis of that subtypes, from August 2006 to December 2007. Results. The study included 19 patients, 14 women and 5 men with mean age 33.4 ± 13.54 years. Of the different subtypes hemiplegic was the most prevalent (11 patients), followed by basilar migraine (3 patients), migraine status (2 patients), retinal migraine (2 patients) and prolonged aura (1 patient). The A3243G mutation in the DNA of peripheral blood leukocytes, which was only evaluated in the study, was not present in any of the samples. Conclusions. The mitochondrial DNA A3243G mutation is not related to the presentation of different subtypes in the population studied. Future clinical trials, with a representative number of patients for each subtypes, may draw conclusions about whether the mitochondrial dysfunction caused by this and other mutations associated with the clinical presentation of this type of migraine.