Hughes then accepted an offer from Brigham Young University (BYU) to begin the International Media Study Program. In 1995, Boutros Boutros Ghali, the Secretary General of the United Nations, requested for Hughes to meet with him. During the meeting, Ghali asked if Hughes would be willing to do some work for the United Nations during the 50th Anniversary of the United Nations. BYU granted Hughes a year leave of absence, and he became an Assistant Secretary General and Director of Communications at the United Nations. In 1996, Neal A. Maxwell called Hughes with concerns about the "Deseret News". Maxwell solicited his advice on improving the paper's circulation. When Hughes returned from the United Nations he began work as a consultant for the "Deseret News". Following his counsel, the paper switched its distribution to morning rather than afternoon, which improved circulation. Following the success of this change, the board of directors asked Hughes to be the editor of the newspaper. Hughes accepted the position, and became the first non-Mormon editor of the "Deseret News". He filled that position until 2007, at which point he returned to BYU as a Professor in the Communications Department. Hughes went to South Africa in 2007 to make a presentation to local media organizations. As of 2012 he continues to write a column for the "Christian Science Monitor". Hughes and his wife Peggy, a BYU alumnus, have a child, Evan. He has two other children – Mark and Wendy – through an earlier marriage to the late Libby Hughes. He has six grandchildren.