Paraformaldehyde (PFA) fixation is a commonly used technique for preserving the cellular and tissue structures of zebrafish embryos for various downstream applications, such as immunohistochemistry, in situ hybridization, and microscopy. PFA crosslinks proteins and stabilizes cellular components, making it ideal for preserving the integrity of samples during experimental procedures. This protocol outlines the steps for performing PFA fixation on zebrafish embryos, which can be adjusted based on the specific requirements of downstream applications.