High voltage pulsing of human skin (approximately 100 V across the skin, 1 ms pulses) has been hypothesized to cause electroporation of the stratum corneum, and to cause large fluxes of drugs and other molecules across the skin, through newly created aqueous pathways. In contrast, iontophoresis (<0.5 mA per cm2, <1 V across the skin) has long been used in transdermal drug delivery, and is believed to involve pre-existing pathways associated with hair follicles and sweat ducts. Either high voltage pulsing or iontophoresis was applied to human, hairless rat, or black rat snake skin. Hairless rat skin contains more hair follicles than human skin, and snake skin does not contain any hair follicles. All three types of skin had comparable electrical resistances at low voltages; however, the iontophoretic transport of charged fluorescent molecules was significant for human and hairless rat skin, but no transport occured across snake skin, indicating that hair follicles and sweat ducts play a major role in iontophoresis. Electroporation caused large molecular transport for all three types of skin, and involved spontaneously forming localized transport regions, not associated with appendages. These experiments thus provide further support for the hypothesis that high voltage pulsing causes electroporation in the stratum corneum, and that this transport mechanism is fundamentally different from iontophoresis.