What aspects of self-assessment can I appeal?

Here are the specific aspects of self-assessment you can appeal against:

Charge-based items (items that create a charge on your SA record):

Penalties:

Fixed penalty for late filing of SA return
Daily penalty for late filing of SA return
Tax geared penalty for late filing of SA return
Tax geared penalty for incorrect SA return
Tax geared penalty for failure to notify chargeability
Tax geared penalty for late payment
Tax geared penalty for excessive reduction of payments on account
Penalty for failure to produce documents
Penalty for failure to keep records
Surcharge (for tax years 2009-10 and earlier)

Assessments and amendments:

Revenue assessments
Revenue amendments to SA return
Jeopardy amendments

Non-charge-based items (no charge created on your record):

HMRC requirement to produce documents
Continuation of a Revenue enquiry
Revenue amendment of a partnership statement

What you CANNOT appeal against:

Your own self-assessment calculation
Revenue determinations
Interest charges
Balancing payments
Payments on Account (though you can claim to reduce them)
Correction notices (but you can reject HMRC’s corrections)
Revenue calculations

Appeal requirements:

Must be made within 30 days of the Notice of Liability (37 days allowed for postal delivery)
Should be in writing (though some appeals accepted by phone or online)
Can be made by you, someone acting in capacity, or an authorized agent
For partnerships: must be made by the nominated partner

Grounds for appeal:

For assessments/amendments:

The assessment or amendment is incorrect
The actual liability has yet to be determined

For penalties:

Fact – e.g., return was filed on time, payment was made on time
Reasonable excuse – e.g., prevented by illness, postal delays, HMRC system issues

The key distinction is that you can appeal HMRC’s actions and decisions, but not your own self-assessment calculations or automatic system calculations.