Hypervariable sites in human mtDNA are readily identified in evolutionary studies and are usually assumed to represent mutational hotspots. Recently, an alternative hypothesis was proposed that holds that hypervariable sites may instead reflect ancient mtDNA mutations that have been "shuffled" among different lineages via recombination. These hypotheses can be tested by examining the evolutionary rates for sites at which new mtDNA mutations are observed; if hypervariable sites are mutational hotspots, then newly arisen mtDNA mutations should occur preferentially at hypervariable sites. Results of this study show that both germline and somatic mtDNA mutations occur preferentially at hypervariable sites, which supports the view that hypervariable sites are indeed mutational hotspots.