The first and second hypervariable regions of the human mitochondrial DNA control region contain two homopolymeric stretches of cytosine (nt 16184–16193 and nt 303–315, respectively). According to the Cambridge reference sequence these homopolymeric stretches are interrupted by thymine (T), at positions 16189 and 310, respectively. Monotonous runs of the same base have been suggested to be hot spots for mutations, probably caused by replication slippage, resulting in length heteroplasmy. This paper describes a rapid method based on restriction cleavage of labelled PCR products encompassing the homopolymeric tract in HVII to quantify the relative proportions of different length variants present in an individual. To compare the accuracy of this method, cloned PCR products from several heteroplasmic individuals have been additionally sequenced.