About half of all our proteins are decorated with carbohydrate structures. These give proteins essential properties such as solubility, half-life, protection against degradation, and are often part of the functional interaction surfaces with other proteins. Proteins in the immune system are no exception; for example, antibodies are completely dependent on carbohydrates to function. Bacteria that live in more or less harmony with us have learned to influence these carbohydrates in different ways during evolution. We have shown that endoglucosidases from pathogenic bacteria can modify carbohydrates on human antibodies with dramatic effects on their immune-stimulating functions. These effects can be exploited to switch off a faulty immune response in several animal models of autoimmune diseases, such as rheumatoid arthritis, multiple sclerosis, autoimmune anemia and autoimmune bleeding disease. Some of our enzymes have also been used as tools for the production and analysis of antibody-based drugs. However, we have only scratched the surface of the probably very extensive arsenal of carbohydrate-modifying enzymes found in our normal flora and pathogenic bacteria. Increasing our knowledge of the structure and function of such enzymes increases our understanding of how bacteria interact with us in health and disease. In addition, new types of enzymes can be of great importance for the modification and analysis of new protein drugs.