Mouse lung tissue can be prepared in a number of different ways before cryosectioning. The method of choice will depend to a large extent on the particular molecular technique that needs to be used. In this study, various preparation techniques were used, and a comparison was made of the results obtained. The aim was to minimize the need to compromise either the molecular analysis or the anatomic evaluation and provide a simple and reproducible method of preparation that allows optimal results in as many situations as possible. (The J Histotechnol 32(4):186–189, 2009)