Botulinum neurotoxin (BoNT) is produced as a large toxin complex (TC) associated with nontoxic nonhemagglutinin (NTNHA) and three hemagglutinin subcomponents (HA-70, -33 and -17). To assess the role of nontoxic components in the oral intoxication of botulinum TCs, we investigated the permeability of serotype D strain 4947 BoNT and its various TC species through cultured Caco-2 cell monolayers. The L-TC species (complexes composed of BoNT, NTNHA, HA-70, HA-33 and HA-17) showed potent permeability through the cell layer, whereas free BoNT, M-TC (BoNT and NTNHA complexes) and M-TC/HA-70 showed little or no permeability. Cell binding tests demonstrated that HA-33/HA-17 complexes bound to cells, whereas other components did not. These findings suggest that BoNT in the 650-kDa L-TC permeates into the cell mainly in an HA-33/HA-17-mediated manner, although free BoNT can permeate into the cell. As free BoNT and M-TC were susceptible to digestion with gastrointestinal juice, it is likely that L-TC species containing HA-33 caused higher oral toxicity in mice than others. We conclude that the HA-33 subcomponent plays a critical role in the permeation of TCs into intestinal epithelium, and that other HA subcomponents protect BoNT against gastrointestinal digestion.