Lee won three titles out of six finals in 2006. He was crowned as the winner of the Swiss Open,[24] Asian Badminton Championships and his third Malaysia Open title. He also reached the final of the Chinese Taipei Open, Macau Open and Hong Kong Open. In the Malaysia Open, Lee fought back from 13–20 down in the rubber match and scored eight match points against Lin Dan, and finally won the game with a score of 23–21 to secure the title.[25] Lee won Malaysia's two gold medals in the badminton event for 2006 Commonwealth Games, in both the men's singles and mixed team events.[26] Lee reached the top spot twice in the Badminton World Federation's world rankings in 2006,[27] and he participated in the World Championships as top seed.[28] However, he was upset by Bao Chunlai of China in the quarter-final despite Lee winning at their previous meeting. The match was also marred by two controversial line calls that were not in favour of Lee.[29]