The experimental manipulation of mid-gestation mouse embryos is an important tool for the study of developmental biology. However, such techniques can be challenging due to difficulties accessing the embryos in utero, and therefore the ability to maintain mid-gestation mouse embryos in vitro has proved invaluable. Described here is an example of a whole embryo culture system, where a serum-free medium is used to support the development of mouse embryos in vitro from embryonic day 10.5 (E10.5) to E11.5. During this time the embryos increase in size and undergo developmental progression, as determined by morphological and molecular criteria. This makes it an ideal environment in which to support and maintain mid-gestation mouse embryos following experimental manipulations. Two applications of this whole embryo culture system are described here. In the first, protein-soaked beads are carefully positioned in the pharyngeal region of an E10.5 embryo, allowing the concentration of specific proteins to be altered within the tissue. In the second technique, morpholino oligonucleotides are electroporated into the pharyngeal region of the embryo at E10.5, creating an efficient system for the knockdown of gene function in the target cells. These techniques demonstrate the use of in vitro techniques to study organogenesis within the pharyngeal region of the mouse embryo, but with some modification they could be adapted to target any region of the endodermal gut tube.