Louis Pasteur, one of the eminent pioneers of microbiology, discovered life without oxygen and identified the first anaerobic pathogenic bacterium. Certain bacteria were found to be responsible for specific diseases. Pasteur was mainly interested in the prevention and treatment of infectious diseases with attenuated pathogens. The collaborators of Pasteur investigated the mechanisms of pathogenicity and showed that some bacterial soluble substances, called toxins, induce symptoms and lesions in experimental animals. Anaerobic bacteriology, which requires specific equipment, has emerged as a distinct part of microbiology. The first objectives were the identification and taxonomy of anaerobes. Several anaerobes producing potent toxins were associated with severe diseases. The investigation of toxins including sequencing, mode of action, and enzymatic activity led to a better understanding of toxin-mediated pathogenicity and allowed the development of safe and efficient prevention and treatment (vaccination with anatoxins, specific neutralizing antisera). Moreover, toxins turned out to be powerful tools in exploring cellular mechanisms supporting the concept of cellular microbiology. Pasteurians have made a wide contribution to anaerobic bacteriology and toxinology. The historical steps are summarized in this review.