The data presented in this article are related to the research article entitled "Design of in vitro skin permeation studies according to the EMA Guideline on quality of transdermal patches" (https://doi.org/10.1016/j.ejps.2018.09.014) (Cilurzo et al., 2018) [1]. In vitro permeation studies are generally carried out by Franz's diffusion cell method using human epidermis as a membrane (Franz, 1975) [2]. The evaluation of membrane integrity is mandatory to assure the quality of the experiments. However, the methods used for this determination are different and the results are strictly dependent on the operative conditions. The article reports the electrical resistance values of human epidermis samples and in vitro skin permeability data of caffeine and benzoic acid. The data are used to establish a cut-off suitable for checking the skin integrity. This information may be useful to enable critical or extended analyses in order to contribute to the development of a compendial method.