Biodegradable nanoparticles have been widely studied as drug carriers in order to increase drug solubility in aqueous media, modify biodistribution, target tissues and organs or control the drug release. Those nanoparticles are, in general, produced as liquid formulations to act as final dosage forms or as intermediate for solid or semi-solid products. Considering the dermatological applications, as medicines or cosmetics, different nanoparticles have been proposed to control the skin penetration of encapsulated lipophilic substances. A point rarely investigated is the penetration of the carrier itself into the skin, independent of the drug penetration profile. In this way, our objective was to correlate the flexibility of the biodegradable nanoparticles to the depth of their skin penetration. To minimize the impact of the chemical composition, the surface chemistry or the shape and size distribution on the results, two kinds of polymeric nanocapsules presenting diverse mechanical properties were produced using almost the same materials and their concentrations. The nanocapsules (NC) and the lipid-core nanocapsules (LNC) were prepared by solvent displacement using Rhodamine B-labeled polymer, oil and surfactants. The only difference in composition between them is the presence of sorbitan monostearate in the latter which was used to have a more rigid nanoparticle as previously reported. NC and LNC had, respectively, mean diameters of 178 and 180 nm and zeta potentials of -11 and -9 mV. The in vitro skin penetration was carried out using Franz cells (pig skin as membrane). Skin samples were observed by confocal laser scanning microscopy (CLSM). NC reached the dermis, while LNC was retained at the outermost layers of the skin. The result was in accordance with the flexibility previously determined for those nanocapsules, in a way that higher flexibility gives deeper penetration. NC can reach the dermis and LNC can act as reservoir systems at the epidermis.