When the slides go from the xylene in the deparaffinizing step to the first alcohol in the hydration sequence, the sections should turn slightly opaque. If there are clear patches present then the deparaffinization was incomplete.
Possible Causes:
- Water still on the slides after the drying oven
- Xylene contaminated with water
Remedies:
- Remove excess water by putting the slides back in the oven or into 100% alcohol
- Change reagents regularly to ensure that the xylenes stay water-free
- Drain slides well before transferring them to the next reagent
