Smallpox Emergency Personnel Protection Act of 2003

Defines a covered injury as an injury, disability, illness, condition, or death arising in a specified time period from the administration of a smallpox vaccine or arising in specified circumstances from an accidental smallpox inoculation. Defines a covered individual as an individual from one of certain professions who is functioning as part of a Federally approved smallpox emergency response plan. Defines an eligible individual as a covered individual who sustains a covered injury from a smallpox vaccine or as an individual who is accidentally inoculated and sustains a covered injury.

Directs the Secretary to create a smallpox vaccine injury table identifying adverse effects that shall be presumed to result from the administration of (or exposure to) a smallpox vaccine and the time period in which the first symptom of each such adverse effect must occur for such presumption to apply.

Requires the Secretary to make payments for medical items and services as reasonable and necessary to treat a covered injury of an eligible individual. Directs the Secretary to provide compensation according to a specified formula to an eligible individual for the loss of employment income incurred due to a covered injury. Provides separately for benefits for permanent and total disability and death.

Amends Public Health Service Act provisions regarding: (1) tort liability for the administration of smallpox countermeasures; and (2) the administration of smallpox countermeasures by health professionals, including to modify the definitions of covered countermeasure, covered person, and qualified person.