Following a recent communication from this laboratory (A. Tivesten et al., J. High Resol. Chromatogr. 1996, 19, 229-233) where on-column chiral derivatization of D- and L-amino acids in micellar electrokinetic chromatography (MEKC) was demonstrated for the first time, we now present further details of the labeling procedure. The basis of the method is the consecutive injection of a sample and the reagent onto the capillary as two discrete plugs. By utilizing their difference in mobility, the zones are mixed by the electrophoretic process in a controllable way. In this way the amino acids are both derivatized within a few seconds and subsequently separated in a single step. Compared with pre-column derivatization, dilution of the original sample is minimized, which is why the method is highly useful for microchemical analytical work, i.e., labeling of nano- to picoliter samples. Four different chiral thiols were compared in this study, 2,3,4,6-tetra-O-acetyl-1-thio-beta-D-glucopyranose (TATG), N-acetyl-L-cysteine (AC), N-acetyl-D-penicillamine (AP), and N-isobutyryl-L-cysteine (IBC). Together with o-phthaldialdehyde (OPA) these constitute the chiral reagent. The reaction rate as well as the spectroscopic and chromatographic properties of the formed derivatives were examined. It was found that the fastest reaction is obtained with OPA/TATG, as was the case with L-alanine (L-ala), and that the rate is greatly affected by the presence and concentration of acetonitrile or methanol. Moreover, OPA/TATG yields superior resolution of D- and L-amino acids over the other OPA/thiol combinations in a sodium dodecyl sulfate (SDS) micellar buffer, whereas the OPA/AC and OPA/IBC-amino acid derivatives have a higher fluorescence quantum yield. With laser-induced fluorescence detection (He-Cd, 325 nm) the mass limit of detection is at the low amol level.