Various lines of evidence demonstrate the involvement of mitochondrial dysfunction in the pathogenesis of Huntington's disease (HD). However, the precise role of mitochondria in the neurodegenerative cascade leading to HD is still unclear. Mitochondrial DNA (mtDNA) haplogroups-specific polymorphisms were previously related to several neurodegenerative diseases. The length of CAG repeat seems to be related to the clinical features of HD, such as age of onset and progression of motor impairment. The basis for the impaired cognitive functions and for the mood changes is less clear. Aim of this study was to determine whether mtDNA polymorphism(s) play the role of "modifier gene(s)" in this disease. In this work we have genotyped predefined European mtDNA haplogroups in 51 patients with HD and 181 matched controls. The frequency of the haplogroups and haplogroup clusters did not differ between the two groups, and no correlation with gender, age of onset and disease status was observed. No significant difference was observed between different haplogroups and haplogroup clusters in the cognitive or motor progression of the disease. Our study does not support any association between mtDNA haplogroups and HD.