A capillary electrophoresis method is developed and validated for the characterization of the affinity and the interaction between aminopenicillanic acid (APS-H) and its derivatives with bile salt micelles. The micellar systems studied contained sodium taurocholate (NaTC) and sodium deoxycholate (NaDC). Using the retention factor k ', functional group selectivity, Gamma (G), is defined as the ratio of the retention factor of a substituted aminopenicillanic acid (APS-R) over the capacity factor of APS-H and the difference in free energy (Delta DeltaG degrees) can be used for the characterization of the affinity and interaction between drugs and micelles. The functional group selectivity is a direct measure of the interaction of the functional group with micelles. The calculated Delta DeltaG degrees value gives information on the partition equilibrium and interaction between drugs and micelles. A positive Delta DeltaG degrees value means that the interaction of a functional group Gamma (G) to the APS-H leads to a decrease in the interaction with the micelles. A negative Delta DeltaG degrees value, on the other hand, has the opposite meaning. The results obtained in this study exhibited that these APS-R compounds have smaller affinity to the micelles compared to unsubstituted APS-H. Furthermore, the log k ' of the drugs in these systems were correlated with the log P-OW in the n-octanol/water system and with log P-G (permeation coefficient).