Abstract We describe a high-quality database containing data from the hypervariable regions HV1 and HV2 on the mitochondrial control region of 103 unrelated Caucasian Danes. Each sample was amplified in duplicates and sequenced twice in both the forward and reverse direction with primer and terminator chemistry, respectively. The data were analysed with the quality assessment program Phred. A total of 94 unique sequences were observed. Most of the observed mutations were T to C or C to T transitions compared to the Cambridge Reference Sequence (CRS).