Mitochondrial DNA (mtDNA) sequencing has been validated as a useful tool for forensic analysis. However, there are several aspects of the analysis which need to be considered in order to evaluate the value of the evidence. One of these aspects is related to heteroplasmy which is the state when two or more mtDNA populations occur in a single individual, cell or mitochondrion. In this report a case is described where the mtDNA profile of the blood sample of a raped woman was compared with the mtDNA profile of a single hair found in the suspect's car. The results obtained show differences in sequence between different portions of the hair and the victim's sequence. These differences are related to various heteroplasmy events. The concordance between the hair sample and the potential source (victim) of this sample is questionable and the strength of the evidence depends on how the sequence information is interpreted by the expert. The discussion of the results emphasises the necessity to evaluate heteroplasmic events in routine forensic work.