Hair from four individuals excavated from burial sites in Pacatnamu, Peru from the Moche (450–800 AD) and Lambayeque (900–1100 AD) periods was sectioned longitudinally and analysed with time-of-flight secondary ion mass spectrometry (ToF-SIMS). An attempt was made to distinguish biogenic and diagenetic contributions to the elemental concentrations in the hair samples. Significant contamination was observed to have penetrated the hair samples from the burial environment. Results from the analyses indicate that the burial environment plays an important role in the postmortem variation in elemental content of hair samples. Various elements demonstrated an ability to permeate through the hair matrix over time. In addition, NaCl and what are believed to be aluminosilicates and mineral sulphates, were observed to have accumulated on the surface of the samples. Degradation of the samples was also suspected due to the presence of molecular fragments, possibly resulting from oxidation of the keratin proteins. The results should assist in the identification of reliable elemental signals in the analysis of ancient hair samples and promote caution when considering elements that are abundant in the burial environment.