Near infrared Fourier transform (NIR-FT) Raman spectroscopy is an analytical, non-destructive technique based on analysis of laser light reflected from the sample. It provides information about the molecular structure of the sample. NIR-FT Raman spectroscopy was employed here to investigate molecular structure of skin samples from mummified bodies from the Chiribaya culture from the Southern Peruvian desert (1500 years before present). In the spectra of dark pigmented mummy in comparison to temporary dried skin a marked loss of protein amide I (1640-1680 cm-1) and amide III (1220-1290 cm-1) band intensities was found, indicating major loss of protein or changes in the secondary protein structure. These molecular changes were less pronounced in the spectra of light pigmented mummies. Moreover a strong peak at 1300 cm-1 and an increased intensity of the peak at 2850 cm-1 was observed. The band at 1300 cm-1 is characteristic for twisting and wagging CH2 vibrations in lipids and the 2850 cm-1 band represents lipid CH stretching vibrations. These spectral changes suggested an increased lipid content in Peruvian mummy skin (light coloured mummies) compared with contemporary skin. We ascribe this increased lipid intensity in the skin of the light coloured Peruvian mummies to embalming, by which means a better preservation is achieved