A skin sample from a South-Andean mummy dating back from the XI(th) century was analyzed using time-of-flight secondary ion mass spectrometry imaging using cluster primary ion beams (cluster-TOF-SIMS). For the first time on a mummy, skin dermis and epidermis could be chemically differentiated using mass spectrometry imaging. Differences in amino-acid composition between keratin and collagen, the two major proteins of skin tissue, could indeed be exploited. A surprising lipid composition of hypodermis was also revealed and seems to result from fatty acids damage by bacteria. Using cluster-TOF-SIMS imaging skills, traces of bio-mineralization could be identified at the micrometer scale, especially formation of calcium phosphate at the skin surface. Mineral deposits at the surface were characterized using both scanning electron microscopy (SEM) in combination with energy-dispersive X-ray spectroscopy and mass spectrometry imaging. The stratigraphy of such a sample was revealed for the first time using this technique. More precise molecular maps were also recorded at higher spatial resolution, below 1 µm. This was achieved using a non-bunched mode of the primary ion source, while keeping intact the mass resolution thanks to a delayed extraction of the secondary ions. Details from biological structure as can be seen on SEM images are observable on chemical maps at this sub-micrometer scale. Thus, this work illustrates the interesting possibilities of chemical imaging by cluster-TOF-SIMS concerning ancient biological tissues. Copyright © 2012 John Wiley & Sons, Ltd.