Electron paramagnetic resonance (EPR) in conjunction with a slow-tumbling simulation was utilized for defining stratum corneum (SC) lipid structure. SC from the back of hairless mouse (HOS:HR-1) was stripped consecutively from one to three or four times using a glass plate coated with a cyanoacrylate resin. Aliphatic spin probes, 5-doxylstearic acid (5-DSA) and 3β-doxyl-5α-cholestane (CHL), were used to evaluate the SC ordering. EPR spectrum of 5-DSA incorporated in the SC demonstrated a characteristic peak for the first strip. A slow-tumbling simulation for 5-DSA showed clear differences in EPR intensities as well as ordering values (S(0)) of the SC for control and terpenes treated SC. The α-terpineol enhanced the permeation of the single chain 5-DSA about three times more than that of the control. However, EPR spectra of CHL in the SC did not show a clear difference for each strip, except for the signal intensity. The results imply that CHL permeates into SC lipid differently from 5-DSA. The enhancement of the 5-DSA is more significant than that of CHL. Therefore, the present results can be useful for various drug administrations via the skin.