A common problem in research laboratories that study the mammalian embryo is the limited supply of live material. For this reason, new methods are constantly being developed and existing methods for in vitro models using cells in culture are being adapted to represent embryogenesis. Three-dimensional fluorescence in situ hybridization (3D-FISH) is an important tool to study where genomic sequences are positioned within nuclei without interfering with this 3D organization. When used in the embryo, this technique provides vital information about the distribution of specific sequences in relation to embryonic nuclear substructures such as nucleolar precursor bodies and chromocenters. In this chapter, we will present a detailed description of FISH in order to perform 3D-FISH in the early preimplantation murine embryos.