The present paper was designed to investigate the effect of varying concentrations of ethanol in receiver solution on the in vitro transdermal permeation of drug across the rat skin. 5-fluorouracil (5-FU) was used as the model drug on account of its good hydrophility, the excised rat skins were treated with different concentration ethanol prepared with normal saline for 12 h, then replaced by normal saline and added the saturated model drug into the donor compartment to determine the transdermal parameters of the drug. Meanwhile, scanning electron microscopy (SEM) was employed to monitor the effect of the different concentration ethanol on the stratum corneum of the rat skin. The ethanol below the concentration of 15% didn't significantly affect the barrier profile of the rat skin, while significant difference of in steady-state transdermal rate and lag times were observed when the concentration of ethanol was 20% or above. The SEM studies indicated that wrinkle of the intact rat skin gradually disappeared and a number of flakes were desquamated from the skin when the concentration of ethanol was above 20%. The results showed that the low concentration of the ethanol (below 15%) didn't obviously affect the excised skin, yet the barrier profile of rat skin would significantly disrupted with the concentration of ethanol above 20%.