The next step after dehydration is called "clearing" and consists of replacing the dehydration solution with a substance that will be miscible with the inclusion medium (paraffin). The term "clearing" comes from the fact that clarifying agents often have the same refractive index as proteins. As a result, when the tissue is completely infiltrated with the clarifier, it becomes translucent. This change in appearance is often used as an indication of the effectiveness of the process.

The clarifying and deparaffinization agents are completely miscible in alcohol and paraffin, which is why these solutions are widely used in histology and cytology. Many steps in the preparation and staining of tissue sections involve clarifying agents, such as, for example, prior to paraffin embedding, when paraffin is removed from the tissue section prior to staining and before mounting between blade and coverslip with mounting medium for long-term observation and storage.

Usually the clarification and dewaxing solutions are based on xylene or toluene. However, given the toxicity of these solvents, there are now alternatives based on hydrocarbons which have the advantage of being much less toxic than xylene but also to be odorless.