For very challenged biological samples, mitochondrial DNA (mtDNA) analysis can often provide results when the more traditional nuclear DNA markers fail. While reliable, the current method of mtDNA analysis by Sanger sequencing is expensive, labor-intensive, and time-consuming and is limited by its inability to quantify mixed samples. The Abbott PLEX-ID™ instrument, which enables analysis of mtDNA amplicons via electrospray ionization mass spectrometry (ESI-MS), produces comparable accuracy and sensitivity while offering a faster and less expensive alternative to Sanger sequencing. Unlike Sanger sequencing, this system is capable of quantifying DNA species and thus may be exploited for evaluating heteroplasmy and, possibly, mixture deconvolution. Validation studies of the PLEX-ID™ mtDNA assay confirmed that the instrument is highly sensitive and capable of yielding reproducible results. Samples commonly encountered in a forensic setting, as well as population samples, were typed correctly. The PLEX-ID™ mtDNA assay yields reliable results for single-source samples, which are the same sample types currently examined in forensic laboratories via Sanger sequencing, at a level that meets or exceeds that of the current method. While the instrument has the demonstrated capability to quantify mixed samples, the specific assay design for mtDNA analysis can be used only in a limited fashion to analyze mixtures due to the formation of chimeric mtDNA products.