The 1999 NCAA Skiing Championships were contested at the Sunday River ski area, near the town of Newry, Maine, at the 46th annual NCAA-sanctioned ski tournament to determine the individual and team national champions of men's and women's collegiate slalom and cross-country skiing in the United States. Defending champions Colorado, coached by , won the team championship, the Buffaloes' fifteenth title overall and fourth as a co-ed team.