Caspases are an evolutionarily conserved family of aspartate-specific cystein-dependent proteases with essential functions in apoptosis and normally exist in cells as inactive proenzymes. In addition to the inflammatory caspases, the initiator and effector caspases have been shown to have an important role in regulating the immune response, but are involved in different ways. We give a brief introduction on the benefit of apoptosis on the clearance of invasive pathogens, and the caspase functions involved in the immune response. Then we construct a working model of caspases during pathogen invasion. A detailed description of the three modes is given in the discussion. These three modes are regulated by different inhibitors, and there may be a novel way to treat intracellular pathogen and autoimmune diseases based on the specific inhibitors.