Microemulsion electrokinetic chromatography (MEEKC) was introduced to evaluate the hydrophobicity of various kinnds of compounds. Using a separation solution consisting of sodium dodecyl sulfate (SDS), 1-butanol, heptane, and a borate-phosphate buffer, the logarithm of the capacity factors, which is proportional to the free energy of transfer into the microemulsion, was high correlated with the logarithm of the octanoywater partition coefficients (log P ow ) rather than with that of the SDS micelle/water partition coefficients measured by micellar electrokinetic chromatography. Even for compounds with hydrogen bond accepting or donating sites, the correlation of the partition coefficients between the microemulsion and the octanoywater system was established without corrections for hydrogen bond effects. Reproducibilities of both run-to-run and batch-to-batch analyses were drastically improved by the use of the migration index concept, itch is analogous to the retention index concept. Furthermore, the thermodynamic behavior of partitioning into the microemulsion was examined. In both the enthalpy and the entropy terms of transfer, the microemulsion system was more similar to a phospholipid vesicle than the octanoywater and SDS micellar systems. Preliminary results of quantitative migration-activity relationship studies, which are defined as quantitative structure-activity relationship studies using the electrophoretic migration data of MEEKC, indicated that this hydrophobic parameter provided slightly better regression to the toxicity data of phenol derivatives than the conventional log P ow . MEEKC rill provide a biologically useful hydrophobic parameter with minimum samples, high reproducibility, wider range of measurement, high resolution, and a single, universal scale