This protocol describes the microimplantation of foreign materials such as schistosome eggs, polymer beads, and other microscopic objects into the small and optically transparent larval zebrafish for the assessment of immune responses, including granuloma formation. This protocol has wide applicability for both fundamental studies on host responses to parasite eggs and other foreign bodies, as well as the testing of potential biomaterials and devices used for human medical implants. For complete details on the use and execution of this protocol, please refer to Takaki et al. (2021a) and (2021b).