Heteroplasmy is the presence of two or more types of mtDNA in a single individual. Heteroplasmy was first observed in humans in association with a mitochondrial disorder; however, heteroplasmy in mtDNA has also been reported in the noncoding control region with greater frequency than had initially been thought. The description of materials and methods for this study addressed the DNA extraction, the PCR amplification , the DGGE, and the sequencing analysis. The screening obtained PCR products from all 3 regions of each of the 480 hair samples from 3 males. The number and mobility of the bands were observed in each sample and compared with the bands from blood samples. The overall frequency of detection for sequence heteroplasmy was 5.8 percent (28 out of 480 hairs) with DGGE and 4.4 percent (21 out of 280 hairs) with sequencing. Sequence heteroplasmy of hair was observed even when the reference blood sample of the individual was homoplasmic. These findings suggest that if there is one nucleotide difference between a questioned hair and known blood sample by sequencing, the interpretation will be inconclusive; however, if the existence of heteroplasmy at such nucleotide position in either the questioned or known samples or both is proved by DGGE or other sensitive detection methods, the interpretation should lead to the possibility of a failure to exclude rather than to an inconclusive result. 2 tables, 1 figure, and 37 references