The invention provides methods for inducing an immune response in a vertebrate host against a protozoan parasite, comprising administering to the host a live protozoan parasite that is genetically engineered to disrupt a stage-specific gene function that is required by the protozoan parasite to establish a secondary infection in the vertebrate host. Representative protozoan parasites belong to the phyla Apicomplexa and Kinetoplastida. The vertebrate host may be a mammal or a bird.