Dry skin symptoms such as scaling and itching are often treated with lipophilic moisturizers. The aim of this study was to investigate the effect of lipophilic moisturizers on the stratum corneum (SC) ultra-structure and lipid organization. Lipophilic moisturizers were applied on the forearms of 4 healthy volunteers for 3 h. Subsequently, the application sites were tape stripped, and selected tape strips prepared for Freeze Fracture Electron Microscopy (FFEM), a method to visualize the SC intercellular lipid parallel to the skin surface. To investigate the effect of lipid moisturizers on the lipid lamellae, isolated SC was pretreated with the lipophilic moisturizers for 24 h prior to performing small angle X-ray diffraction (SAXD) measurements. Additionally, the lipid organization of mixtures prepared with ceramides, cholesterol, free fatty acids and lipophilic moisturizer in a 2:1:1:1 molar ratio were studied using SAXD. The FFEM data (in vivo) as well as the SAXD data (in vitro) show that the lipophilic moisturizers do not change the lipid lamellar organization in the SC. Addition of 20% m/m lipophilic moisturizer to the ceramide:cholesterol:free fatty acids mixture did not inhibit the formation of the long periodicity phase, the characteristic lamellar phase in the SC, even though there was clear evidence that two of the three moisturizers were at least partially incorporated in the long periodicity phase. Concluding, all findings suggest that the lipophilic moisturizers investigated in this study do not drastically change the lamellar organization of the SC intracellular lipid matrix, but that the moisturizers form separate domains in the SC, as was visualized by FFEM.