Lectin affinity electrophoresis was applied to the separation of charged, fluorescent conjugates of disaccharides. Four fluorescent conjugates were prepared by reductive amination of α-d-Man-(1→3)-d-Man, α-d-Gal-(1→4)-d-Gal, α-d-Gal-(1→6)-d-Glc, and β-d-Gal-(1→4)-d-Glc in the presence of 7-amino-1,3-naphthalenedisulfonic acid. These charged fluorescent-disaccharide conjugates all have identical molecular weight and in the absence of conconavalin A lectin failed to separate either by agarose or by polyacrylamide gel electrophoresis. In the presence of either free or immobilized concanavalin A, agarose gel electrophoresis and polyacrylamide gel electrophoresis could separate the fluorescent conjugate of α-d-Gan-(1→3)-d-Man from that of α-d-Gal-(1→4)-d-Gal, α-d-Gal-(1→6)-d-Glc, and β-d-Gal-(1→4)-d-Glc. © 1992.