Findings show that more than half of the detected sequences (17 of 20, 15 of 20, and 14 of 20) showed homoplasmy derived from a variation in the heteroplasmy proportion when only 10 copies of template mtDNA samples were amplified and analyzed. In addition, with products amplified from one or several white blood cells (WBCs), several previously undetected heteroplasmies were detected. These findings show the risk associated with using highly sensitive mtDNA techniques in forensic investigations due to the variable proportions of heteroplasmy or nucleotide substitutions that can possibly be detected from a very small biological sample. In many cases, heteroplasmy can lead to confusion when the sequences are compared; for example, in some cases of maternal-individual identification, the ratio of heteroplasmy is sometimes significantly different between generations, and the haplotypes of each sequence are apparently mismatched. Consequently, this report advises that in analyzing mtDNA for identification, forensic scientists should recognize the potential risks, in that different haplotype of mtDNA sequences derived from potential heteroplasmy or from polymerase misincorporation can be potential problems when a very small amount of template DNA is amplified using high-sensitivity PCR. The description of materials and methods addresses DNA extraction from bloodstain samples, quantification of mtDNA, WBC samples, nested PCR, sequencing analysis, the measurement of proportion of each heteroplasmy, and the screening of heteroplasmy. 2 tables, 3 figures, and 25 references