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The 30-year-old now finds himself at the center of a brewing controversy that threatens to derail not only his career but the troubled sport of cycling altogether.
Landis can expect the next several days, weeks and even months to be filled with counter-analysis, complicated tests and hearings as he enters the tricky roads of testing sanctions.
How do anti-doping controls work at the Tour?
Each day, the stage winner and overall leader are tested, along with two randomly selected riders. Urine samples typically are collected, but sometimes blood samples also are taken.
The samples are then divided into two vials, the "A" and "B" samples, which are then transported to an officially sanctioned laboratory for analysis. This time, the samples were taken to the Châtenay-Malabry labs near Paris. It usually takes three-to-five days for the initial "A" sample to be tested.
If results come back positive, a strict protocol is followed. The rider, his team, his national governing body and the national anti-doping agency are notified immediately. A counter-analysis is conducted within three-to-five days.
The rider has the right to witness the counter-analysis or simply waive the second test and admit guilt. If the second "B" sample confirms the result of the first test, the test is considered a positive doping test. If the "B" sample contradicts the first test, the test comes back negative and the rider is cleared.
After winning Stage 17, Landis gave urine samples that led him to where he is now.
Why are two samples collected?
There's always a chance of human error, a screwup in the testing procedure or contamination to skew the results or give a "false-positive." Those odds are reduced to almost zero when two tests from the same sample are conducted separately.
All told, nearly 200 blood and urine tests were conducted during the 2006 Tour. So far, Landis is the only rider to fail an "A" sample. Officials said all the other samples already have been tested, so there won't be any more cases from this year's Tour.
What happens next?
Landis is still waiting for the results of the "B" sample, expected within the next few days. If the second test comes back negative, Landis safely retains his Tour de France crown, but perhaps with an asterisk next to his name.
If the second test supports the first test, the implications are fast and immediate. First, he would be considered positive for a failed doping test. Then, he likely would be fired from his Phonak team, which already has confirmed it will do just that if the second test is positive.
Landis will have a right to appeal the ruling to the Court of Arbitration for Sport (see below). If he loses there or chooses not to appeal, he would be sanctioned and stripped of his Tour victory. Second-place rider Oscar Pereiro would be elevated to Tour winner.
Will there be sanctions?
Under tough anti-doping rules, a first-time offense draws an automatic two-year suspension. A second offense results in a ban for life. Landis has never failed a doping test in his seven-year career, so he would face a two-year racing ban.
Another wrinkle are new rules that won't allow sanctioned riders to return to one of the 20 elite "ProTour" teams for an additional two years, essentially doubling their ban and forcing them to race for minor squads that don't participate in Europe's most important races, such as the Tour de France and one-day classics like the Paris-Roubaix race.
How is testosterone detected?
Testosterone is a naturally occurring hormone, and there is no surefire way to detect it. Instead, anti-doping controls use a system called mass spectrometry. Testosterone and epitestosterone, another naturally occurring hormone, are usually within a constant balance of each other, called the T/E ratio.
Most people have a ratio between 1-to-1 and 2-to-1, but cycling's governing body has set a threshold at 4-to-1 to allow for riders with naturally high testosterone levels. Major spikes in the testosterone levels in relation to the epitestosterone can suggest manipulation or doping, triggering a red flag for testers.
Unscrupulous athletes have learned to inject epitestosterone into their systems to bring balance to the ratio and mask the use of testosterone. There was no information released about Landis' T/E ratio. To further complicate things, Landis also will undergo an endocrine test to determine his naturally occurring levels of testosterone.
Can Landis challenge the decision?
Landis can contest the allegations to the Court of Arbitration for Sport, located in Lausanne, Switzerland. Kind of a Supreme Court for doping disputes, the arbitration panel is the last chance for athletes to appeal their cases. Many athletes have had doping charges against them thrown out because of inconsistencies using the T/E ratio as a basis for testosterone detection. That process can take several months.
Can Landis be stripped of his title?
Yes, if he's found positive and either loses his CAS battle or outright admits to doping, he will lose his Tour crown. He would be the first outright Tour winner to lose the title for doping charges. In the Tour of Spain last year, overall winner Roberto Heras also saw his title stripped after testing positive for banned blood booster EPO.