There is an increasing trend to use mitochondrial DNA (mtDNA) analysis in criminal investigations where only limited amounts of DNA are available. However, analysis of the mtDNA control region has the drawback of low discrimination power, due to the lack of recombination that results from uniparental (maternal) inheritance. As a strategy to increase discrimination, a number of typing assays detecting variation in the mitochondrial coding region have been developed. In this study, several of these assays are evaluated for their discriminatory capacity using data obtained from 495 complete Caucasian mtDNA sequences. In order to add a local geographic perspective to this evaluation, we have also sequenced and analysed the entire mtDNA from 20 individuals of Swedish origin. We find that the coding region assays are very useful for resolving sequences with identical HVI/HVII regions. The best-performing coding region assay was able to discriminate 46% of the resolvable sequences, compared to 20-30% for the other coding region assays we evaluated.