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1. The haplogroups and polymorphisms of mitochondrial (mt) DNA are associated with longevity. This association is highly geographically dependent. The aim of the present study was to determine the relationship between mtDNA haplogroups, single nucleotide polymorphisms (SNPs) and longevity in the Chinese Uygur population. 2. Ninety-eight Uygur Chinese subjects aged over 90 years (vitality 90+) and 117 healthy young controls living in the Xinjiang Uygur Autonomous Region of China were chosen for the present study. Frequencies of mtDNA haplogroups and SNPs in the subjects were analysed using polymerase chain reaction. The entire mtDNA genome was sequenced and the mtDNA haplogroups and SNPs were determined. 3. Nine haplogroups were identified in the Chinese Uygur population and the frequency of haplogroup J was higher in control subjects than in the vitality 90+ group (odds ratio = 0.384; 95% confidence interval = 0.163–0.906; P = 0.025). Interestingly, most of the SNPs were in the D-loop region, with frequencies higher in the control group than in the vitality 90+ group. 4. In conclusion, mtDNA haplogroups are potentially associated with longevity in the Uygur Chinese population and the D-loop region is strongly involved in ageing-related events. [ABSTRACT FROM AUTHOR]