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The effectiveness of the skin barrier underlies the outer layer of the skin: the stratum corneum (SC). However, in several skin diseases this barrier is impaired. In two inflammatory skin diseases, atopic eczema and Netherton syndrome, an increased level of monounsaturated fatty acids (MUFAs) has been observed as opposed to healthy skin. In the present study, we aimed to investigate the effect of MUFAs on the lipid organization and skin lipid barrier using an in vitro model membrane system, the stratum corneum substitute (SCS), mimicking the SC lipid composition and organization. To achieve our goal, the SCS has been prepared with increasing levels of MUFAs using various chain length. Permeation studies and trans-epidermal water loss measurements show that an increment of MUFAs reduces the lipid barrier in the SCS. The increased level of unsaturation exerts its effect by reducing the packing density in the lipid organization, while the lamellar phases are not affected. Our findings indicate that increased levels of MUFAs may contribute to the impaired skin barrier in diseased skin.