We have assessed the histological preservation of naturally degraded human hair shafts, and then assayed each for levels of amplifiable mitochondrial DNA and damage-associated DNA miscoding lesions. The results indicate that as sample histology is altered (i.e. as hairs degrade) levels of amplifiable mitochondrial DNA decrease, but no correlation is seen between histology and absolute levels of mitochondrial DNA miscoding lesions. Nevertheless, amplifiable mitochondrial DNA could be recovered across the complete range of the histological preservation spectrum. However, when template copy number is taken into consideration, a correlation of miscoding lesions with histology is again apparent. These relationships indicate that a potential route for the generation of misleading mitochondrial sequence data exists in samples of poor histology. Therefore, we argue that in the absence of molecular cloning, the histological screening of hair may be necessary in order to confirm the reliability of mitochondrial DNA sequences amplified from hair, and thus represents a useful tool in forensic mitochondrial DNA analyses.