We report: a highly sensitive and rapid strategy for characterizing biological toxins based on capillary electrokinetic chromatography with multiphoton-excited fluorescence, In this approach, aflatoxins B-1, B-2, and G(1) and the cholera toxin A-subunit are fractionated in similar to 80 s in a narrow-bore electrophoretic channel using the negatively charged pseudostationary phase, carboxymethyl-beta-cyclodextrin. The aflatoxins-highly mutagenic multiple-ringed heterocycles produced by Aspergillus fungi-are excited at the capillary outlet through the simultaneous absorption of two to three 750-nm photons to yield characteristic blue fluorescence; cholera toxin A-subunit, the catalytic domain of the bacterial protein toxin from Vibrio cholera, is excited through an unidentified multiphoton pathway that apparently includes photochemical transformation of an aromatic residue in the polypeptide, The anionic carboxymethyl-beta-cyclodextrin, used to chromatographically resolve the uncharged aflatoxins, enhances emission hom these compounds without contributing substantially to the background. Detection limits for these toxins separated in 2.1-mu m-i.d. capillaries range from. 4.4 zmol (similar to 2700 molecules) for aflatoxin B-2 to 3.4 amol for the cholera toxin A-subunit. Larger (16-mu m-i.d.) separation capillaries provide concentration detection limits for aflatoxins in the 0.2-0.4 nM range, severalfold lower than achieved in 2.1-mu m capillaries, These results represent an improvement of > 10(4) in mass detectability compared to previously published capillary separations of aflatoxins and demonstrate new possibilities for the analysis of proteins and peptides.