As mucus is highly hydrated, special care has to be taken to preserve this in histological preparations during immunostaining. Here, we describe how to fix tissues in such a way that the mucus is preserved in paraffin-embedded tissue. We also describe how the major macromolecular components in the mucus, the mucins, are immunostained and how bacteria can be localized in preparations with preserved mucus by fluorescent in situ hybridization.