The aim of this study was to investigate the local changes in the ultrastructure of human skin after iontophoresis, using cryo-scanning, transmission and freeze fracture electron microscopy in human skin in vitro and in vivo. Human dermatomed skin was subjected to passive diffusion for 6 hours followed by nine hours of iontophoresis at 0.5 mA/cm2. The skin was processed and examined using both cryo-scanning electron microscopy (Cryo-SEM) and transmission electron microscopy (TEM). In addition, iontophoresis patches were applied to healthy volunteers for 3.5h with 0.5h of passive delivery followed by 3h of iontophoresis at a current density of 0.25 mA/cm2. Subsequently, a series of tape stripping were performed, which were visualized by freeze fracture transmission electron microscopy (FFTEM). In vitro, the cryo-scanning electron microscopy study revealed that electric current induced changes in the water distribution in the stratum corneum. Transmission electron microscopy showed no local changes in the ultrastructure of the stratum corneum; however, layers of detached corneocytes were frequently observed especially at the anodal site. In vivo, there was no evidence of perturbation of the stratum corneum lipid organization; however, changes in the fracture were noticed deeper in the stratum corneum at the anodal side, indicating a weakening of the desmosomal structure. The in vitro/in vivo studies suggest that iontophoresis results in the formation of intercellular water pools (in vitro observation) and a weakening of the desmosomal structure (in vivo observation) only in the upper part of the stratum corneum. However, no changes in the lipid organization were observed in vitro and in vivo at the current densities of 0.5 and 0.25 mA/cm2, respectively. Therefore, even at relatively high current densities, no drastic changes in the ultrastructure of the stratum corneum are observed. As far as structural changes in stratum corneum are concerned iontophoresis is therefore a safe method at the experimental conditions we used.