Various mutations in the mitochondrial tRNA(Leu)(UUR) gene give rise to a variety of neurological disorders. Among these, mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS syndrome) are frequently associated with a tRNA(Leu)(UUR) mutation at nucleotide position 3243 of the mitochondrial DNA. A supplementary clinical feature seen in these patients is headache in early life. Recently, a tRNA(Leu)(UUR) mutation at nucleotide position 3243 has been found in a patient presenting with cluster headache. This led us to examine the mitochondrial genomes of 22 patients presenting with cluster headache. None of the patients harboured the reported tRNA(Leu)(UUR) mutation or any other length variations of the mtDNA. Cluster headache is most likely not causally associated with the A3243G mutation of the mitochondrial DNA.