The Tour began with a prologue in Strasbourg, on the French-German border, and ended on Sunday July 23 in Paris. The distance of the course (run counterclockwise around France) was 3,657 km (2,272 mi). The race was the third fastest in average speed. Along the way, the cyclists passed through six different countries including France, The Netherlands (a stop at Valkenburg in Stage 3), Belgium (at Huy, Stages 3 and 4), Luxembourg (at Esch-sur-Alzette, Stages 2 and 3), Germany (though not stopping there, Stage 1) and Spain (Pla-de-Beret, Stage 11). The presentation of the course was made by the new director of Le Tour, Christian Prudhomme. For the first time since the 1999 edition, there was no team time trial.
The event, as with some of the Tours of the late 1990s, was marred by doping scandals. Prior to the tour, numerous riders – including the two favourites Jan Ullrich and Ivan Basso – were expelled from the Tour due to their link with the Operación Puerto doping case.
After the Tour, the apparent winner, Floyd Landis, was found to have failed a drug test after stage 17; Landis contested the result and demanded arbitration. On September 20, 2007, Landis was found guilty and suspended retroactive to January 30, 2007 and stripped of the 2006 Tour de France title making Óscar Pereiro the title holder. Landis appealed the decision to the Court of Arbitration for Sport which upheld the ban.
In the most controversial scandal since the 1998 tour, thirteen riders were expelled from the tour on the eve of Strasbourg prologue to the 93rd edition stemming from a Spanish doping scandal. Jan Ullrich and Ivan Basso, two favourites to win the race, were among those excluded from the Tour along with podium candidate Francisco Mancebo and Alberto Contador (who would return to win the following year, 2007). 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. It was also the first Tour since 1999 that did not contain a past champion.
The initial doping controversy foreshadowed the contested outcome of the 2006 Tour involving the race leader Floyd Landis who was found guilty of doping.
American Floyd Landis was initially awarded the victory in the closest three-way finish in the race's history to date. Floyd's final time was 89h 39'30".
While Landis was a leading favorite even before the Spanish doping scandal came to light, 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.
But the following day, during Stage 17, Landis set a very high pace on the first climb of the day that no other rider could match. 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.
On September 20, 2007, Landis' doping accusation was upheld by an arbitration panel deciding between him and USADA and will be banned for two years. In response to this, International Cycling Union formally stripped him of his 2006 Tour de France title. Second place finisher Óscar Pereiro was officially declared the winner. The only previous Tour de France winner to be disqualified was 1904 Tour de France winner Maurice Garin.
Stage 17 was originally won by Floyd Landis, who also wore the yellow jersey on the 19th and 20th stage. After the court's decision to forfeit all his results in the 2006 Tour de France, Carlos Sastre became the winner of the 17th stage, and Cyril Dessel and Óscar Pereiro should be considered having led the general classification as shown in the table.
After the retirement of then seven-time winner Lance Armstrong, the main contenders for the overall win were expected to be Ivan Basso from Team CSC, the 2005 runner-up; and Jan Ullrich from T-Mobile Team, the third man on the podium in 2005, winner in 1997, and the only previous winner still racing. However, both Ullrich and Basso were suspended by their teams on June 30 after UCI told T-Mobile and Team CSC that the riders were involved in the anti-doping investigation in Spain.
Francisco Mancebo of the French team AG2R Prévoyance, who finished fourth last year and sixth the year before, was also suspended by his team, and subsequently announced his retirement. Alexander Vinokourov would have been the only returning rider with a top-five finish from last year's race. However, his team, Astana–Würth, was forced to pull out of the race because they would not be able to start with the minimum of six riders.
The 2006 Tour also saw the return of former yellow jersey holder and three-time stage winner David Millar (Saunier Duval–Prodir) after serving a two-year ban for admissions of the use of the drug EPO, which was discovered in a police search of his house before the 2004 Tour de France, in June 2004.
^"United States Anti-Doping Agency vs Floyd Landis"(PDF). UNITED STATES ANTI-DOPING AGENCY. 2007-09-20. Retrieved 30 December 2010. The violation of the UCI Rules having occurred as a result of an In-Competition test will result under UCI Articles 256 and 257.2 in the automatic disqualification of the Athlete's results in the 2006 Tour de France and forfeiture of any medals, points or prizes.