Immunoprecipitation (IP) is a powerful method to isolate a target protein and its interacting partners from a complex biological sample. This protocol is specifically designed for tuning immunoprecipitation experiments to isolate GFP-tagged proteins from zebrafish embryos. The protocol includes the preparation of zebrafish extracts, matrix preparation, antibody incubation, and the subsequent detection of immunoprecipitated proteins by SDS-PAGE and Western blotting.