Clostridium difficile produces two major toxins referred to as toxins A and B. These are thought to be primarily responsible for the virulence of the bacterium and the major contributors to the pathogenesis of antibiotic-associated gastrointestinal disease. The molecular organization and control of expression of toxins A and B is now starting to be understood, and the cellular mechanism of action of both toxins, glucosylation of Rho family proteins, has been discovered. Other factors, such as production of proteolytic and hydrolytic enzymes, expression of fimbriae and flagella, chemotaxis and adhesion to gut receptors, and production of capsule, may all play a part in pathogenesis by facilitating colonization or by directly contributing to tissue damage, or both. Differential expression between strains of various combinations of these colonization and virulence factors may explain the apparent variability in virulence of C. difficile strains.