The influence of palmitic acid on n-octanol/water partition coefficient (log P) of selected amino acids, alanine, glycine, proline, hydroxyproline, seine, valine, threonine and lysine, was measured at a wide range of pH. A parabolic shape curve was obtained in every case (pH vs. Deltalog P), with maximum depending on the amino acid. In each case in the presence of palmitic acid, the apparent partition coefficient increased. To check the possible mechanism of extraction of amino acids into n-octanol phase in the presence of palmitate additionally, the influence of an amount of counter ion on partition coefficient of lysine was investigated. The results suggest that the enhanced partitioning of lysine results from the ion pair formation with palmitate. The ion pair stratum corneum-lipid membrane transport of the amino acids was investigated as well, using palmitate as a counter ion. The apparent permeability coefficients were enhanced significantly by palmitic acid at pH 7.4. As many substances (e.g. organic solvents, unsaturated fatty acids, etc.) are penetration enhancers which change the structure of intercellular lipid, the influence of palmitic acid on membrane was investigated. After pretreatment of membrane with palmitic acid, no changes in permeation of alanine were observed. Investigations suggest the enhanced permeation of amino acids via ion pairing. The method for prediction of pH in which the possibility of ion pairing is the highest was developed as well.