Intercellular lipid structures in the human stratum corneum are responsible for the barrier function of skin. For a full understanding of the structural organization of the human skin barrier and the properties of the barrier, structural and physicochemical parameters of skin lipids and lipid systems were investigated on a molecular level. In this study the thermotropic behaviour three main lipid classes of human stratum corneum, i.e., free fatty acids, cholesterol, and ceramides, were characterized using differential scanning calorimetry (DSC), X-ray powder diffraction, FT-IR and FT-Raman spectroscopy. The combination of these methods has offered the possibility to study the thermotropic response in the head groups and the arrangement of the hydrocarbon chains of different ceramides and mixtures ceramides with fatty acids or cholesterol. Additional, the influence of water on the molecular organisation of ceramides was studied. It has been shown that various arrangements can be formed by skin lipids depending on the molecular structure of the ceramides and the composition of the model systems.