During direct sequencing of the first hypervariable segment of the human mitochondrial control region, we identified one individual with a heteroplasmic point mutation at nt 16,256. We used primer extension to analyze the proportions of each mitochondrial haplotype in peripheral blood, buccal cells, and single hair roots from this individual and from eight members of his maternal lineage. Significant levels of heteroplasmy were found in only three individuals, and, in these cases, the proportions of each haplotype were similar in both blood and buccal cells. From the changes in mitochondrial haplotypes within mother-offspring pairs, we calculated that the most likely size of a mitochondrial bottleneck during development was 1-27 segregating units. However, highly variable levels of heteroplasmy were found in single hair roots, even among roots from the same individual. We analyzed a large number of hair roots from one individual and found that the proportion of one haplotype was within a range of 9% to > 99% in different roots. Roots originating from within a small patch of skin had haplotype proportions as variable as those from different areas of skin.