Hemolytic uremic syndrome, a serious complication of Shiga toxin-associated diarrhea, is rare before 6 months of age. Immunologic and nonimmunologic factors present in human milk may partially explain this observation. In prior studies, we have demonstrated that human milk contains Gb3, the receptor for the B subunit of Shiga toxin, and also contains secretory IgA (sIgA) against the toxin. We therefore sought to determine the relative importance of milk glycolipid and toxin-specific sIgA in toxin binding. We studied two populations that differed in their frequency of exposure to Shiga toxin. Human milk samples obtained from healthy donors from Boston and Buenos Aires were separated by centrifugation into aqueous (antibody enriched) and cream (glycosphingolipid enriched) fractions. An emulsion of equal volumes of aqueous phase or cream layer of each sample and purified Shiga toxin was incubated, and the amount of free toxin present in each was determined by enzyme immunoassay. The cream layers bound 85%+/-2 (mean +/- SE) (Argentina milk samples) and 86%+/-1 (Boston milk samples) of Shiga toxin. In contrast, the soluble fraction in samples from Buenos Aires, a population expected to frequently have antibodies to Shiga toxin, bound more toxin (48%+/-2) than did this fraction in samples from Boston, an area where toxin exposure is infrequent (30%+/-3) (P < 0.0001). Toxin-binding lipids present in human milk are biologically active and may contribute to the putative protective effect of human milk. In a population frequently exposed to Shiga toxins (Argentina), protection may be due to both immune (sIgA), and nonimmune (lipid) factors present in human milk. In a population infrequently exposed to Shiga toxins, cream fraction-associated glycolipids represent the major toxin binding activity in human milk.