Alexander Vinokourov, another race favourite, was not linked to the doping scandal, but was forced to withdraw when the eligible riders on his Astana-Würth Team fell below the minimum starting requirement of six.

Because of this and the retirement of then-seven-time consecutive winner Lance Armstrong, this year's Tour started without the top five riders from the 2005 edition.

As a result of the drug scandal, many believed Spaniard Alejandro Valverde (Caisse d'Épargne), or the Americans Floyd Landis (Phonak), Levi Leipheimer (Gerolsteiner), or Australian Cadel Evans (Davitamon–Lotto) would probably win the race.

[7] The highest point of elevation in the race was 2,642 m (8,668 ft) at the summit of the Col du Galibier mountain pass on stage 16.

[8] Due to the developing doping case known as Operacion Puerto several top tier riders were denied entry to the 2006 Tour including Jan Ullrich, Joseba Beloki, Alberto Contador, Ivan Basso and indirectly, as his team did not have enough eligible riders, Alexander Vinokourov.

The ITT was won handily by Serhiy Gonchar who claimed the maillot jaune with Floyd Landis finishing in 2nd in the Stage, as well as moving up the standings into 2nd place in the overall.

The top GC Contenders wouldn't change places until Stage 13 when Jens Voigt and Óscar Pereiro outlasted Manuel Quinziato and Sylvain Chavanel in a four-man breakaway that finished about 30 minutes ahead of the Peloton.

Pereiro jumped everyone to take the overall lead by about 1:30 over Landis and Dessel and around 2:30 ahead of Menchov and Evans with Sastre over 3:00 back.

Stage 16 was won by Michael Rasmussen as Pereiro took over the race lead with Sastre jumping up to 2nd, Kloden taking over 3rd and Landis coming entirely unhinged and dropping outside the top 10.

In Stage 17 however, Landis made the potentially catastrophic decision to attack off the front of the Peloton entirely on his own over 100 km from the finish in pursuit of the morning Breakaway bunch.

Before long he caught the escapees, rode with the break for a while, then attacked off the front with only Patrice Halgand and Patrik Sinkewitz able to stay with him for any length of time, though without doing any work being as Halgand was nearly cooked, and Sinkewitz was teammates with two riders placed higher than Landis in Kloden and Michael Rogers.

Floyd Landis won the 2006 TDF by defeating all of the other GC Contenders except for Kloden taking the Yellow Jersey back for the 3rd and final time.

Landis would be stripped of his only Tour de France victory soon after winning it following a confirmed failed drug test after Stage 17 and Óscar Pereiro would be declared the winner.

While Landis was a leading favourite even before the Spanish doping scandal came to light,[16] in an epic eight-minute loss of performance in Stage 16, it appeared he had lost all hope to finish on the podium, much less win.

He then caught a breakaway group that had escaped earlier, passed them, and continued to the finish line solo, making up almost all of his deficit, ending up 30 seconds behind yellow jersey wearer Óscar Pereiro, which he made up with an extra minute in the final Stage 19 time trial.

[18] On 20 September 2007, Landis' doping accusation was upheld by an arbitration panel deciding between him and USADA and will be banned for two years.

Not long after getting surgery for his hip, while still on crutches, Landis briefly participated in a 2008 documentary film about steroids and performance-enhancing drugs titled Bigger, Stronger, Faster*.

He stated that he slept at an altitude of 13,000 feet, felt proud of what he accomplished in the 2006 Tour and at that time, still considered himself the winner.

[26] The riders in the team that lead this classification were for the first time identified with yellow number bibs on the back of their jerseys.

[23] In addition, there was a combativity award given after each mass start stage to the rider considered, by a jury, to have "made the greatest effort and who has demonstrated the best qualities of sportsmanship".

[27] There were also two special awards each with a prize of €5000, the Souvenir Henri Desgrange, given in honour of Tour founder and first race director Henri Desgrange to the first rider to pass the summit of the Col du Galibier on stage 16, and the Souvenir Jacques Goddet, given in honour of the second director Jacques Goddet to the first rider to pass the summit of the Col du Tourmalet on stage 11.