Micellar electrokinetic chromatography (MEKC) was evaluated as a new technique for the rapid estimation of octanol-water partition coefficient (logKow). Retention measurements for more than 40 reference pesticides with varied structural characteristics and hydrophobicity were carried out in two MEKC systems, based on sodium dodecyl sulfate (SDS) and sodium cholate (SC), respectively. To enable an accurate determination of capacity factors in the SC-MEKC system, cypermethrin (a synthetic pyrethroid insecticide) was utilized instead of Sudan III as the SC micelle tracer, since a few highly hydrophobic pesticides were found to elute after Sudan III. The linear correlation between logarithmic capacity factor (logk̃′1) and logKow in the two systems was examined. It was found that, under the typical buffer condition (10 mM sodium phosphate with 60 mM surfactant, pH 7.0), the SDS-MEKC system provided a somewhat wider dynamic range for hydrophobicity (logKow from −1.0 to 4.5). However, the correlation of logk̃′i with logKow was not very high when all the reference pesticides were included in one single calibration set. For the SC-MEKC system, the dynamic range for logKow was in the range of 1.0–5.5, and a good linear correlation existed between logk̃′i and logKow, even when all reference pesticides were incorporated into a single calibration group. By comparing the regression line of the reference pesticides with that of a group of simple aromatic derivatives, it was discovered that molecular size and functionality posed a less significant effect on the measurement of logKow in the SC-MEKC system than in the SDS-MEKC system. Thus, SC-MEKC shall be the system of choice for the estimation of logKow. The typical error on logKow determination using the current MEKC technique was within 0.5 units, suggesting that MEKC can be a valuable complement to reversed phase – high performance liquid chromatography (RP-HPLC) for the indirect determination of logKow. Besides maintaining all the advantages of the HPLC approach, the MEKC technique showed some unique benefits, such as better inter-column reproducibility, higher throughput, and less handling of toxic pesticides and solvents.