The Justice Department said it will base its appeal to the 8th U.S. Circuit Court of Appeals (search) on two aspects of this month's ruling.
The department said it will challenge U.S. District Judge Richard Kopf's ruling that the ban, while containing an exception to save the life of the mother, makes no such exception for the health of the woman.
The department also said it would challenge Kopf's ruling that the ban poses an undue burden on a woman's right to an abortion.
The case is expected by many legal experts to eventually reach the U.S. Supreme Court.
President Bush signed the abortion ban last year but it was not enforced because three federal judges agreed to hear constitutional challenges in simultaneous non-jury trials.
Kopf ruled that Congress ignored the most experienced doctors in determining that the banned procedure would never be necessary to protect the health of the mother — a finding he called "unreasonable."
His ruling followed similar decisions by federal judges in New York and San Francisco.
The Justice Department already has filed an appeal of the San Francisco ruling.