deparaffinization

Deparaffinization is the process of removing paraffin wax from tissue sections that have been embedded in paraffin for microscopic analysis. Paraffin provides support for thin sections and facilitates handling during sectioning, staining, and mounting; however, most stains and molecular assays require access to hydrated tissue, so the paraffin must be removed and the tissue rehydrated prior to staining.

In routine histology and immunohistochemistry, deparaffinization is typically achieved by immersion of mounted slides in a nonpolar organic solvent such as xylene, or in alternative xylene substitutes, followed by rehydration through a graded ethanol series to water. A common sequence is two changes in xylene (5–10 minutes each), then a sequence of 100%, 95%, 70%, and 50% ethanol, with brief rinses between steps. After hydration, the tissue is ready for antigen retrieval or staining. For RNA or DNA assays in paraffin sections, dewaxing is critical to allow access of reagents to nucleic acids.

Laboratories increasingly use xylene-free dewaxing agents, such as limonene-based solvents or other substitutes, to reduce toxicity and environmental impact. Some protocols employ heat-assisted dewaxing or perform deparaffinization as part of automated stainers.

Safety and handling: xylene and some substitutes are flammable and toxic; appropriate ventilation, gloves, and waste disposal procedures are required. The exact timing and solvent choice depend on the tissue type, embedding medium, and downstream assay.