Oriented stratum corneum model lipid membranes were used to study the influence of the short chain ceramides (CER)[NP] and [AP] as well as the impact of the lipophilic penetration enhancer molecules oleic acid (OA) and isopropyl myristate (IPM) on the lipid nanostructure. The influence of the enhancer molecules were studied using specifically deuterated OA and IPM and neutron diffraction. H NMR spectroscopy was used to study the impact of the ceramides’ degree of order within the stratum corneum model lipid membranes. It was found that CER[NP] forms two very stable phases with high resistance against temperature increase. Phase B showed unusual hydration behavior as no water uptake of this phase was observed. The H NMR spectroscopic measurements showed that CER[NP] based ternary model system had a higher state of lamellar order in comparison to CER[AP] based lipid matrix. The studies confirmed that the short chain ceramides, particularly CER[NP], have a very high impact on the integrity of the Stratum corneum lipid bilayers. The penetration enhancer OA has not influenced the repeat distance of the model membrane based on CER[AP], and was not able to induce a phase separation in the investigated lipid matrix. However, a disorder and a fluidisation of the model membranes were observed when OA was incorporated. IPM showed the same effect but two phases (assigned as phase A and B) appeared, when IPM was used as penetration enhancer and incorporated into the model membrane. Furthermore, two arrangements of IPM were identified in phase A using deuterated IPM. A model of the nanostructure of the Stratum corneum lipid membranes is presented.