Human skin equivalents (HSEs) mimic human skin closely, but show differences in their stratum corneum (SC) lipid properties. The aim of this study was to determine whether isolation of primary cells, which is needed to generate HSEs, influence the SC lipid properties of HSEs. For this purpose, we expanded explants of intact full thickness human skin and isolated epidermal sheets in vitro. We investigated whether their outgrowths maintain barrier properties of human skin. The results reveal that the outgrowths and human skin have a similar morphology and expression of several differentiation markers, except for an increased expression of keratin 16 and involucrin. The outgrowths show a decreased SC fatty acid content compared with human skin. Additionally, SC lipids of the outgrowths have a predominantly hexagonal packing, whereas human skin has the dense orthorhombic packing. Furthermore, the outgrowths have lipid lamellae with a slightly reduced periodicity compared with human skin. These results demonstrate that the outgrowths do not maintain all properties observed in human skin, indicating that changes in properties of HSEs are not caused by isolation of primary cells, but by culture conditions.