Taxpayer and Fairness Protection Act of 2003

Taxpayer and Fairness Protection Act of 2003 - Amends the Internal Revenue Code to revise various abusive tax shelter provisions, including: (1) clarification of the economic substance doctrine; and (2) imposition of new, and revision of existing, tax shelter-related penalties.

Provides for the prevention of corporate expatriation to avoid U.S. income tax.

Revises provisions respecting: (1) the earned income tax credit; (2) specified penalties and interest, including estimated tax penalty and interest; (3) collection procedures; (4) Internal Revenue Service (IRS) employee misconduct; (5) Tax Court authority and jurisdiction; (6) family business; (6) suspension of tax-exempt status for terrorist organizations; (7) confidentiality and disclosure; and (8) IRS user fees.

Authorizes grants for low-income return preparation clinics.

Amends the Temporary Extended Unemployment Compensation Act of 2002 with respect to the applicability of Federal-State unemployment assistance agreements.