Standard in vito skin percutaneous penetration methods using excised guinea pig dorsal skin were employed, to characterize the penetration of a water-insoluble drug: tenoxicam (TEX), and a water-soluble drug: diclofenac sodium salt (DFS), enhanced by phosphatidylglycerol (PG); and an attenuated total reflectance fourier transform infrared (ATR-FTIR) spectroscopy was used to analyze the molecular mechanism of the drug penetration route. The C-H bond stretching absorbance frequency shift in the stratum corneum (SC) induced a higher and a broader absorbance, and the shift was dependent on the PG concentrations. The percutaneous penetration of TEX was dependent on the PG concentration (up to 6%). The enhancing mechanism of PG to TEX may not only increase the diffusion coefficient (D) and the partition coefficient (K) in the percutaneous TEX penetration but also increase fluidity of the route (intercellular lipid domain) for TEX, while that of PG to DFS, excepting 1%, PG system, may be increasing the D value in the percutaneous DFS penetration only. The percutaneous penetration of DFS was not dependent on the PG concentrations. Furthermore, the percutaneous penetration of TEX was proportional to the C-H bond stretching absorbance frequency shifts. In contrast, the percutaneous penetration of DFS was not proportional to the C-H bond stretching absorbance frequency shifts. Furthermore, the accumulation of TEX in skin was proportional to the C-H bond stretching absorbance frequency shifts. The striking parallel between the enhancement of the percutaneous penetration of TEX and the measured SC lipid fluidity shifts caused by PG, suggests that the transdermal water-insoluble drug penetration may be ultimately related to the SC lipid structure. Overall, these results suggest that PG mainly affects the intercellular lipid pathway (lipid-rich domains).