Genetically Engineered Crop and Animal Farmer Protection Act of 2003

Genetically Engineered Crop and Animal Farmer Protection Act of 2003 - Requires a biotech company that sells any genetically engineered animal, plant, or seed that will be used in the United States to: (1) provide the purchaser with written notice of possible legal and environmental risks of such article's use (such disclosure shall neither relieve the company from liability, nor be construed to create purchaser liability); and (2) disclose any technology fees to the Secretary of Agriculture, and not charge fees that are higher than those outside the United States.

Sets forth related contract prohibitions and limitations.

Directs the Secretary to: (1) identify which plants are outcrossed pollinators and make such information available to affected sellers and purchasers; and (2) issue rules to require mitigationtrategies for predominately outcrossed crops.

Amends the Federal Insecticide, Fungicide, and Rodenticide Act to direct the Administrator of the Environmental Protection Agency to: (1) establish the best achievable resistance plan for plant-incorporated pesticides engineered to include toxins derived from the bacterium Bacillus thuringiensis (Bt); (2) revoke Bt registrations not in plan compliance; and (3) reduce a pesticide's use if it is determined to be facilitating Bt-toxin resistance in pests.

Prohibits: (1) labeling seeds as non-genetically engineered if the Secretary determines such seeds contains genetically engineered material; (2) manufacture, sale, or planting of genetically engineered or chemically induced non-fertile seeds; and (3) loan discrimination against a producer who refuses to use genetically engineered plants or animals.

Authorizes, with respect to violations under this Act,: (1) the Secretary to assess civil penalties; and (2) citizen civil actions against the Secretary, a Federal agency, or an individual.