Specific allegations

In 2004, sports reporters Pierre Ballester and David Walsh jointly published a book alleging Armstrong had used performance-enhancing drugs (L. A. Confidentiel - Les secrets de Lance Armstrong). It contains allegations by Armstrong's former masseuse Emma O'Reilly who claimed that Armstrong once asked her to dispose of used syringes and give him makeup to conceal needle marks on his arms. Another key figure in the book, Steve Swart, claims that he and other riders, including Armstrong, began using drugs in 1995 while they were members of the Motorola team, a claim since denied by other team members. Allegations in the book were reprinted in the UK newspaper The Sunday Times in a story by deputy sports editor Alan English in June 2004. Armstrong subsequently sued the newspaper for libel, which settled out of court after a High Court judge in a pretrial ruling stated that the article "meant accusation of guilt and not simply reasonable grounds to suspect." The newspaper's lawyers issued the following statement: "The Sunday Times has confirmed to Mr Armstrong that it never intended to accuse him of being guilty of taking any performance-enhancing drugs and sincerely apologised for any such impression." (See also in The Guardian). Armstrong later dropped similar lawsuits in France.
On March 31, 2005, Mike Anderson filed a brief in Travis County District Court in Texas, as part of a legal battle following his termination in November 2004 as an employee of Armstrong. Anderson worked for Armstrong for two years as a personal assistant. In the brief, Anderson claimed that he discovered a box of Androstenine while cleaning a bathroom in Armstrong's apartment in Girona, Spain. While Androstenine is not on the list of banned drugs, the substances androstenedione and androstenediol are listed. However, Anderson stated in a subsequent deposition that he had no direct knowledge of Armstrong using a banned substance. Armstrong denied the claim and issued a counter-suit. The two men reached an out-of-court settlement in November 2005, the terms of the agreement undisclosed.
On August 23, 2005, L'Équipe, a major French daily sports newspaper, reported on its front page under the headline "The Armstrong Lie" that urine taken from the cyclist during the prologue and five stages of the 1999 Tour de France had tested positive for EPO in recent testing conducted as part of a research project into EPO testing methods. This claim was based on an investigation in which they claimed to be able to match samples from the 1999 Tour that were used to hone the EPO test to Armstrong. The world governing body of cycling, Union Cycliste Internationale (UCI), did not begin using a urine test for EPO until two years later, in 2001. Armstrong immediately replied on his website, saying, "Unfortunately, the witch hunt continues and tomorrow’s article is nothing short of tabloid journalism. The paper even admits in its own article that the science in question here is faulty and that I have no way to defend myself. They state: 'There will therefore be no counter-exam nor regulatory prosecutions, in a strict sense, since defendant’s rights cannot be respected.' I will simply restate what I have said many times: I have never taken performance enhancing drugs."
In June 2006, French newspaper Le Monde reported claims made by Betsy and Frankie Andreu during a deposition that Armstrong had admitted using performance-enhancing drugs to his physician just after brain surgery in 1996. The Andreus' testimony was related to litigation between Armstrong and SCA Promotions, a Texas-based company that was attempting to withhold a $5-million bonus; this was eventually settled out of court with SCA paying Armstrong and Tailwind Sports $7.5 million, to cover the $5-million bonus plus interest and lawyers' fees. Armstrong later issued a statement suggesting that Betsy Andreu may have been confused by possible mention of his post-operative treatment which included steroids and EPO that are routinely taken to counteract wasting and red-blood-cell-destroying effects of intensive chemotherapy. The Andreus' allegation was not supported by any of the eight other people present, including Armstrong's doctor Craig Nichols,  or his medical history, although according to Greg LeMond (who has been embroiled with his own disputes with Armstrong), there exists a recorded conversation in which Stephanie McIlvain, Armstrong's contact at Oakley Inc., said to Greg LeMond, "You know, I was in that room. I heard it."
In July 2006, the Los Angeles Times published an in-depth story on the allegations raised in the SCA case. The report cited evidence presented at the trial including the results of the LNDD test and an analysis of these results by an expert witness. From the LA Times article: "The results, Australian researcher Michael Ashenden testified in Dallas, show Armstrong's levels rising and falling, consistent with a series of injections during the Tour. Ashenden, a paid expert retained by SCA Promotions, told arbitrators the results painted a "compelling picture" that the world's most famous cyclist "used EPO in the '99 Tour." Ashenden's finding were disputed by the Vrijman report, which pointed to procedural and privacy issues in dismissing the LNDD test results. The LA Times article also provided in-depth information on the testimony given by Armstrong's former teammate Steven Swart, Frankie Andreu and his wife Betsy, and Instant messaging conversation between Andreu and Jonathan Vaughters regarding blood-doping techniques in the peloton. Vaughters later signed a statement disavowing the comments and stating he had: "no personal knowledge that any team in the Tour de France, including Armstrong's Discovery team in 2005, engaged in any prohibited conduct whatsoever." Andreu signed a statement affirming the conversation took place as indicated on the Instant messaging logs submitted to the court. The SCA trial was decided in favor of Armstrong, and the LA Times reported: "Though no verdict or finding of facts was rendered, Armstrong called the outcome proof that the doping allegations were baseless." The LA Times article provides a comprehensive review of the disputed positive EPO test, allegations and sworn testimony against Armstrong, but notes that: "They are filled with conflicting testimony, hearsay and circumstantial evidence admissible in arbitration hearings but questionable in more formal legal proceedings."
In September 2006, Frankie Andreu and another unnamed teammate were reported to have made recent statements that they used EPO during the 1999 Tour de France. This was the same tour, and the same drug, at issue in the controversy with the World Anti-Doping Agency. While both teammates are reported as saying they never saw Armstrong use EPO, Armstrong at once attacked the article, describing it as a "hatchet job."


Investigation

In October 2005, UCI appointed Dutch lawyer Emile Vrijman to investigate the handling of urine tests by the French national anti-doping laboratory, LNDD. Vrijman was the head of the Dutch anti-doping agency for ten years; since then he has worked as a defense attorney defending high-profile athletes against doping charges. Vrijman's report "cleared" Armstrong because of improper handling and testing[25][26]. The report said that tests on urine samples were conducted improperly and fell so short of scientific standards that it was "completely irresponsible" to suggest they "constitute evidence of anything." The recommendation of the commission's report was that no disciplinary action should be taken against any rider on the basis of the LNDD research. It also called upon the WADA and LNDD to submit themselves to an investigation by an outside independent authority. The WADA rejected these conclusions and is considering legal action.