He made his first entry into World Championship tournaments at the FIDE World Chess Championship 1999 held in Las Vegas, defeating Christian Bauer 1½-½ but losing to eventual quarter-finalist Sergei Movsesian after rapid tiebreaks 2½-1½. In January 2000, Leko faced the winner, FIDE World Champion Alexander Khalifman in a six-game match held in Budapest, which he won 4½-1½.