Alito was joined in his dissent by Justices Antonin Scalia and Clarence Thomas and Chief Justice John G. Roberts Jr.
The court in 1977 ruled that the death penalty for rapists was unconstitutional under the 8th Amendment's ban on cruel and unusual punishment. That decision involved the rape of a 16-year-old female, whom the court considered an adult.
More than a decade ago, Louisiana made rape a capital crime if the victim was younger than 12. The state said it has sought the death penalty in only five cases, twice obtaining a capital verdict.
Several other states, including Texas, Georgia and South Carolina, have similar laws, but they require that the assailant have committed a second, separate offense before the death penalty is an option.
The defendant in the case on which the court ruled Wednesday, Patrick Kennedy, has maintained his innocence. He had been offered life in prison if he pleaded guilty. He refused and was sentenced to death in 2003.
He and his stepdaughter originally said that two boys assaulted her in March 1998 in the backyard of their home in Jefferson Parish, across the Mississippi River from New Orleans. But police found inconsistencies in Kennedy's story and blood on sheets inside the home. The girl was badly injured and required surgery.
Kennedy, 43, will still face life in prison with no possibility of parole. His lawyers plan to appeal his conviction.
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Tribune staff writer John D. McCormick in Chicago contributed to this report.