the identification and characterisation of dna damage is of great importance to molecular research and has significant implications for clinical and forensic fields. from the moment of cell death, dna incurs many forms of damage, chemical and physical modifications, and fragmentation. this occurs primarily during the biological decay of a sample, but can then stabilise depending on the depositional environment. the damage and degradation continues if there is disruption or excavation of the sample through to the molecular analyses and storage in the laboratory. fluorescent labelled multiplex pcr coupled with real time pcr has been developed to characterise secondary dna damage incurred duirng laboratory analyses. this has been investigated by analysis of the stability and degradation of dna placed under different storage conditions. parameters, including storage buffer, storage temperature, and dna exposure to repeated freeze/thaw cycles, were examined and analysed using a multiplex augmentation analysis system. it was shown that finding the optimal storage conditions of dna dramatically increased the stability and longevity of molecules for pcr analyses. assessment of the quantity and quality of dna from ancient or degraded samples allows for method improvements, provides indicators for further analysis, and can provide authentication of ancient or degraded dna by quantity, quality and augmentation. this assessment of dna species in archaelogical and forensic samples provides integral information for fast and resourceful use of limited and low-copy number dna samples.