Knowledge Base › Troubleshooting Atlas › H&E staining
Patchy / uneven staining
Also known as: uneven H&E, blotchy staining
What it looks like
Areas of the section stain strongly while others are pale; uneven colour across or between slides.
Where it usually appears: Incomplete dewaxing, dirty reagents, or sections drying out.
Likely causes
- Incomplete dewaxing/rehydration (residual wax repels stain)
- Sections dried out during the run
- Reagent levels low so slides not fully immersed
- Contaminated or exhausted reagents
Immediate checks
- Extend/refresh the dewax and rehydration steps
- Top up reagent levels so slides are fully covered
- Avoid letting slides dry between steps
Corrective action
- Dewax fully and re-stain
- Filter or replace contaminated reagents
Preventive action
- Adequate oven/dewax step
- Maintain reagent levels and rotation
- Keep the stainer serviced
This atlas is for educational purposes for laboratory professionals. It does not replace your institutional SOPs, manufacturer instructions, validated protocols or pathologist judgment. Adapt any action to your laboratory and equipment.
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