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In order to cross the skin barrier several techniques and carrier systems were developed to increase skin penetration of topical dermatics and to reduce systemic adverse effects by avoiding systemic application. Ultra-flexible vesicles, e.g. invasomes and core–multishell (CMS) nanotransporters are efficient drug delivery systems for dermatological applications. Electron paramagnetic resonance (EPR) spectroscopic techniques were used for the determination of localization and distribution of the spin label 3-carboxy-2,2,5,5-tetramethyl-1-pyrrolidinyloxy (PCA; log P = −1.7) within the carrier systems and the ability of the carriers to promote penetration of PCA into the skin. The results show an exclusive localization of PCA in the hydrophilic compartments of the invasome dispersion and the CMS nanotransporter solution. PCA penetration was enhanced 2.5 fold for CMS and 1.9 fold for invasomes compared to PCA solution. Investigation of penetration depth by step-wise removal of the stratum corneum by tape stripping revealed deepest PCA penetration for invasomes. UV-irradiation of PCA-exposed skin samples revealed that the spin label is still reactive. In conclusion novel polymer-based CMS nanotransporters and invasomes can favor the penetration of PCA or hydrophilic drugs. This offers possibilities for e.g. improved photodynamic therapy.