A comparative analysis of carbohydrate libraries derived from cell lines binding E-selectin was used to identify endogenous protein-associated carbohydrate ligands for E-selectin. Three structures, which together constitute less than 1% of the total cell surface protein-associated carbohydrate, were unique to cell lines capable of binding E-selectin, including neutrophils and the monocytic cell line U937. All are tetra-antennary N-linked structures, with a sialic acid alpha 2 --> 3 galactose beta 1 --> 4 (fucose alpha 1 --> 3) N-acetyl glucosamine beta 1 --> 3 galactose beta 1 --> 4 (fucose alpha 1 --> 3) N-acetyl glucosamine lactosaminoglycan extension (sialyl-di-Lewis X [S-diLe(x)]) on the arm linked through the C4 residue on the mannose. While all contained the expected 3-SLe(x) sub-structure, these native structures have an additional fucosylated lactosamine unit. Direct evidence that these S-di-Lex-containing structures are high-affinity ligands for E-selectin came from the use of recombinant soluble E-selectin-agarose affinity chromatography. These three carbohydrate structures bound specifically to the E-selectin column, while 3-SLe(x) itself does not bind under identical conditions.