Clostridium difficile toxins A and B together are responsible for the symptoms of pseudomembranous colitis. Both toxins intoxicate cultured cells by the same mechanism but they differ in cytotoxic potency, toxin B being generally 1,000 times more potent than toxin A. Don and T84 cells were used to determine differences in the intoxication process exerted by both toxins. Three main differences were identified: (a) the specific binding of radiolabeled toxins to the cell surfaces correlated with the cytotoxic potency, (b) toxin B was found to have a 100-fold higher enzymatic activity than toxin A, and (c) toxin A was found to modify an additional substrate, Rap. The relative contribution of (a) and (b) to the difference in cytotoxic potency was determined by microinjection of the toxins. The differing enzymatic activities turned out to be the main determinant of the difference in cytotoxic potency, whereas the difference in binding contributes to a lesser degree. These findings are discussed in the context of the pathophysiological role of the toxins.