We present a mathematical model of mitochondrial inheritance evolving under neutral evolution to interpret the heteroplasmies observed at some sites. A comparison of the levels of heteroplasmies transmitted from mother to her offspring allows us to estimate the number N(x) of inherited mitochondrial genomes (segregating units). The model demonstrates the necessity of accounting for both the multiplicity of an unknown number N(x), and the threshold , below which heteroplasmy cannot be detected reliably, in order to estimate the mitochondrial mutation rate mu(m) in the maternal line of descent. Our model is applicable to pedigree studies of any eukaryotic species where site heteroplasmies are observed in regions of the mitochondria, provided neutrality can be assumed. The model is illustrated with an analysis of site heteroplasmies in the first hypervariable region of mitochondrial sequence data sampled from Adélie penguin families, providing an estimate N(x) and mu(m). This estimate of mu(m) was found to be consistent with earlier estimates from ancient DNA analysis.