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Topical therapies for nail diseases are limited by keratinized cells in the human nail plate. An optimal permeation enhancer would not only improve drug delivery through the nail plate, but would also open new possibilities for treating neighboring target sites if systemic circulation is reached. The aim of the present work was to identify permeation enhancers and to improve the understanding of physicochemical parameters that influence drug permeation. Caffeine served as the model drug, and formulations were prepared in water and 20% (v/v) ethanol/water solutions. Tested enhancers were urea, dimethyl sulfoxide (DMSO), methanol, N-acetyl-l-cysteine (NAC), docusate sodium salt (DSS), boric acid, and fungal proteins, such as hydrophobins. Permeability studies employed cadaver nails in modified Franz-type diffusion cells. The permeability coefficient of caffeine in ethanol/water was determined to be 1.56E−08 cm/s and was improved to 2.27E−08 cm/s by the addition of NAC. Formulations containing either methanol or DMSO showed the highest permeability coefficients in the range of 5–7.5E−08 cm/s. Enhancers could be classified according to their permeation enhancement: methanol > class II hydrophobins > DMSO > followed by class I hydrophobins and urea. Ethanol at a concentration of 20% (v/v) in water did not influence swelling of nail samples. Hydrophobins are suggested to be efficient in drug delivery through the nail plate.