In the 2006 Tour de France, he finished well overall but he was not team leader; that honour went to the Russian, Denis Menchov. Rasmussen won the mountains classification for the second year and claimed stage 16 in the process. On Stage 16 he broke away after 4 km and took the Souvenir Henri Desgrange on the Col du Galibier (2645 m), winning 5000 euros. He led over all the climbs and won stage 16 by more than a minute on Carlos Sastre of Team CSC. In Paris he wore the polka dot jersey as leader of the mountains classification while holding his newly born child, who was in a polka-dot shirt and cap.