In the embedding process, tissue samples in their cassettes and liquid embedding material (such as paraffin wax) are placed into molds and allowed to harden. The hardened blocks containing the tissue samples are then ready to be sectioned. Embedding can also be accomplished using frozen, non-fixed tissue in a water-based medium, usually a water-based glycol or resin.

In the sectioning phase, the tissue is sliced into very thin (3-5µm; 1000µm = 1mm) sections using a microtome. These slices, usually thinner than the average cell, are then placed on a glass slide for staining. Frozen tissue embedded in a freezing medium is cut on a microtome in a cryostat.

Routine staining is done to give contrast to the tissue being examined. Haematoxylin and Eosin (H and E) are the most commonly used stains in histology.

Haematoxylin is combined with a metal mordant, such as aluminum, and the haematoxylin-aluminium complex is used to stain cell nuclei blue/black. Eosin is the most widely used counterstain in the routine staining of tissue sections. The best staining with eosin occurs at pH 4.5 to 5 and, when used properly, multiple shades of pink can be obtained. Erythrocytes, collagen, and the cytoplasm of epithelial or muscle cells should stain different shades of pink when using eosin. After staining the sections need to be mounted to protect the specimen, which requires the use of mounting media and a coverslip.