The 1999 NCAA Division I Cross Country Championships were the 61st annual NCAA Men's Division I Cross Country Championship and the 19th annual NCAA Women's Division I Cross Country Championship to determine the team and individual national champions of NCAA Division I men's and women's collegiate cross country running in the United States. In all, four different titles were contested: men's and women's individual and team championships. The two individual champions were, for the men, (South Alabama, 30:06.6) and, for the women, (Wisconsin, 16:39.5).