Emmert was named Chancellor of LSU in 1999. He led the creation of the "Flagship Agenda," an effort credited with moving the university significantly forward in its standing as an academic institution, an effort that is still credited with advancing the university in very significant ways. During his tenure the academic preparation of entering freshmen increased substantially. Enrollment from across the country increased as well. LSU's research profile improved as a result of new research initiatives, particularly in computer science, marine and coastal science, and basic sciences. A number of academic construction projects commenced, including buildings and renovations for music and dramatic arts, marine biology and coastal studies, biology, residence halls, and the student union. Fund raising projects were begun that have resulted in dramatic improvements in the Ogden Honors College, the E.J. Ourso College of Business and the College of Engineering. Improvements were made to athletic facilities, most notably the creation of the Cox Communications Academic Center, renovation and expansion of Tiger Stadium, and a new state-of-the-art enclosure for the campus mascot, Mike the Tiger, that has become a major attraction for visitors to campus. Emmert’s wife, DeLaine Emmert, was very engaged in these fund raising efforts. State support for the university reached a then-historic high during Emmert's tenure.