Abstract: Objects To study the relationship between the mitochondrial DNA (mtDNA) D-loop mutation and Huntington Disease. Methords (CAG)n repeat size and mtDNA D-loop fragment deletion or insertion were detected by PCR-DNA sequencing in two HD pedigree. Results normal individuals （CAG）n≤18 times， patient’s abnormal n≥40 times. There were no fragment deletion and insertion in the mitochondrial control region. Conclusions: Big fragment’s recombination in mtDNA control region maybe isn’t the important factor in HD pathogenic mechanism.