The respiratory system consists of the nasal cavity, larynx, trachea, major airways and lung parenchyma. In the mouse, three stages of development are recognized in the embryonic lung. The cutting of standardised upper respiratory tract sections and the recognition of the normal histologic anatomy of cell populations within those sections is very important as it enables more accurate interpretation of the effects on cell types that will vary with location of the level of the section. Tracheal instillation of the lungs with buffered formalin at necropsy is an accepted technique to improve the histology of the pulmonary architecture and should be used for all studies in mice.