The octanol-water partition coefficients of seven anthocyanins (in neutral form, pH = 7.0) were measured by means of MEKC. A new iterative method for the estimation of migration time of electroosmotic flow (EOF) and micelles in MEKC is presented. This calculation is based on Gauss-Newton linearization of the dependence between migration indices and migration times of a set of suitable standards and the application of an advanced statistical evaluation procedure. The values of partition coefficients obtained with the aid of an iterative process are compared with values obtained on use of EOF and micelle markers.