The molecular mechanisms controlling Drosophila embryogenesis are among the best-studied examples in animal development. Whereas the formation of developmental pattern in embryos was intensely examined in the past three decades, the cell biological basis of morphogenesis is now entering the center stage of the research on fly embryos. A fundamentally important procedure has always been to determine the subcellular localization of proteins in embryos by immunolabeling. The challenge of the commonly used whole mount-staining procedures is to balance a good structural preservation during fixation and allow at the same time the penetration of the antibodies through the tissue. Different procedures have been developed that allow the preservation of distinct compartments of the cell and thus, optimize for the specific subcellular localization of proteins. This chapter provides a general immunolabeling protocol with variations suitable for a broad panel of antigens.