Lee picked up only one title in 2002 and 2003, reaching the final of the 2003 Malaysia Open (his first final of a major tournament) where he was defeated by Chen Hong of China.

Lee then secured two titles in 2004, the Malaysia Open and the Chinese Taipei Open. Lee gained a spot for the 2004 Olympic Games in Athens. In his first Olympic appearance, Lee defeated Ng Wei of Hong Kong in the first round. His journey ended in the second round when he was defeated by Chen Hong. Lee scored another two titles in 2005, his second Malaysia Open title and the Denmark Open. Lee won a bronze in his first appearance in the world meet, the 2005 World Championships after losing to eventual winner Taufik Hidayat in the semi-final.

Lee won three titles out of six finals in 2006. He was crowned as the winner of the Swiss Open, 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. 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. Lee reached the top spot twice in the Badminton World Federation's world rankings in 2006, and he participated in the World Championships as top seed. 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.

During the 2007 season, Lee failed to reach the final of the Malaysia Open for the first time in five years. He also suffered an early exit in five competitions afterward. Later on that season he took the Indonesia Open crown, his first title since the 2006 Malaysia Open after reuniting with former coach Misbun Sidek from Li Mao. His performance at the second half of the year was solid, as he achieved three titles in the Philippines Open, the Japan Open, and the French Open. He also managed to reach the final of the China Open and Hong Kong Open, despite his knee injury haunting him on both occasions. Lee won all matches he played in the Sudirman Cup in June, despite Malaysia finishing just fifth in the tournament. Lee's low point of the year was in the World Championships, despite the tournament being held in front of his home crowd and his solid performance during the second half of the year, he was defeated in the third round by Indonesia's Sony Dwi Kuncoro. Lee took a swipe at chief coach Yap Kim Hock soon after the defeat, claiming that Yap treated him indifferently and was putting pressure on his preparation for the championships.

2013[edit]
2010[edit]
Career[edit]
2002–2007[edit]