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The purpose of this study was to construct isotretinoin-loaded SLN (IT-SLN) formulation with skin targeting for topical delivery of isotretinoin. PRECIROL ATO 5 was selected as the lipid of SLN. Tween 80 and soybean lecithin were used as the surfactants to stabilize SLN. The hot homogenization method was performed to prepare the drug-loaded SLN. The various formulations were characterized by photon correlation spectroscopy and all the SLN formulations had low average size between 30 and 50 nm. Transmission electron microscopy studies showed that the IT-SLN formulation had a spherical shape. All the formulations had high entrapment efficiency ranging from 80% to 100%. The penetration of isotretinoin from the IT-SLN formulations through skins and into skins were evaluated in vitro using Franz diffusion cells fitted with rat skins. The in vitro permeation data showed that all the IT-SLN formulations can avoid the systemic uptake of isotretinoin in skins, however the control tincture had a permeation rate of 0.76 ± 0.30 μg cm−2 h−1 through skins. The IT-SLN consisting of 3.0% PRECIROL ATO 5, 4.0% soybean lecithin and 4.5% Tween 80 could significantly increased the accumulative uptake of isotretinoin in skin and showed a significantly enhanced skin targeting effect. The studied IT-SLN showed a good stability. These results indicate that the studied IT-SLN formulation with skin targeting may be a promising carrier for topical delivery of isotretinoin.