Francisc George, a defender of Catholic orthodoxy with extensive experience in Rome, won overwhelmingly in a vote at the fall meeting of the nation's bishops.
He had served the last three years as the conference vice president. The prelate holding that job customarily is elected to the top post.
George succeeds Bishop William Skylstad, of Spokane, Washington, who is ending his term. Bishop Gerald Kicanas of Tucson, Arizona, was elected as the new vice president.
The conference president does not set policy, but acts as a national spokesman for the bishops and represents the U.S. church in meetings at the Vatican.
George, 70, will take over at a time of diminishing influence for the group. The conference has cut jobs and committees to streamline its work and save money.
Bishops have said that the funds they turn over for conference work are badly needed in their home dioceses. They blame rising costs for health care and salaries, multimillion-dollar abuse settlements and other expenses.
In Chicago, George succeeded the beloved Cardinal Joseph Bernardin, who died of pancreatic cancer in 1996. In George's first year as archbishop, disgruntled priests dubbed him "Francis the Corrector." But he went on to become a leader among American prelates, promoting traditional Catholic teaching and working with Vatican agencies on improving how the church responds to clergy sex abuse.
However, the lay reform group Voice of the Faithful and the Survivors Network of those Abused by Priests have criticized his record on the molestation crisis.
The archdiocese waited months to remove an accused parish priest in Chicago, the Rev. Daniel McCormack, who was criminally charged last year and pleaded guilty to sexually abusing five boys ages 8 to 12. George has acknowledged that he failed to act soon enough in McCormack's case.
George, a member of the religious order Missionary Oblates of Mary Immaculate, is known for his intellect. He holds doctorates in philosophy and theology. For more than a decade, he served in Rome as vicar general of the Oblates, building ties within the Vatican.