Immunosuppressive treatment plays a crucial role in the management of autoimmune and autoinflammatory diseases. Knowledge about the ensuing immune deficits resulting from these therapies as well as common infections in immunocompromised patients should be familiar to all doctors involved in the prescription and administration of immunosuppressive drugs. Comprehensive pretreatment screening, regular monitoring both during and following treatment as well common sense preventive measures, such as vaccination can help further minimise the risk of infection.