Farm Disaster Emergency Assistance Act of 2003

Farm Disaster Emergency Assistance Act of 2003 - Directs the Secretary of Agriculture to provide: (1) emergency financial assistance to agricultural producers who have incurred qualifying 2001 or 2002 crop losses due to weather or related conditions; and (2) payments to livestock producers who have incurred 2001 and 2002 losses in an emergency-designated county, with discretionary set-asides for the American Indian livestock program.

Permits producers with qualifying losses in both years to elect to receive payments in either, but not both, of such years.

Makes producers ineligible for crop disaster assistance if they did not: (1) get Federal crop insurance for insurable commodities; and (2) file required paperwork and pay related fees for noninsurable commodities. Sets forth waiver provisions.

Directs the Secretary to transfer specified Commodity Credit Corporation amounts to a certain account established to encourage domestic consumption and foreign exportation of agricultural commodities.