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Contador was kept out of the 2006 Tour de France due to alleged connections with the Operación Puerto doping case. However, he and four other members of his team at the time, Astana-Würth, were eventually cleared of all charges on 26 July 2006 by the Spanish courts and later two out of the five (including Contador) were cleared by the UCI. Each received a written document signed by Manuel Sánchez Martín, secretary for the Spanish court, stating that "there are not any type of charges against them nor have there been adopted any type of legal action against them."
In May 2006, a document from the summary of the investigation (Documento 31) was released. In it, Contador's initials (A.C.) were associated with a hand-written note saying, "Nada o igual a J.J." (Spanish for "Nothing or like J.J."). J.J. were the initials of Jörg Jaksche, who later admitted to be guilty of blood doping prepared by the Spanish doctor Eufemiano Fuentes in 2005. Contador was questioned in December 2006 by the magistrate in charge of the Puerto file. The rider declared to Judge Antonio Serrano that he did not know Eufemanio Fuentes personally. According to French daily Le Monde, he refused then to undergo a DNA test that would have judged whether or not he had any link to the blood bags that were found in the investigation.
On 28 July 2007, Le Monde, citing what it claimed was an investigation file to which it had access, stated that Contador's name appeared in several documents found during Operación Puerto. According to some sources, Contador's name is mentioned on a list of then-Liberty Seguros teammates that appear on a document later identified as a list of training schedules for members of the team. A second reference includes initials of riders’ names that appeared on another training document, although neither of those two references could be linked to doping practices.
On 30 July 2007, German doping expert Werner Franke accused Contador of having taken drugs in the past and being prescribed a doping regimen by Fuentes, who was connected with Operación Puerto. He passed his allegations on to the German authorities on 31 July 2007. Contador denied the accusations, saying "I was in the wrong team at the wrong time and somehow my name got among the documents." On 10 August, Contador publicly declared himself to be a clean rider in face of suspicions about his alleged links to the Operación Puerto blood doping ring.
Conta er altså frikjent av både spanske myndigheter og UCI, ASO har vel heller ingen problemer med ham. For de som har fulgt med Contador gjennom karrieren hans så er det heller intet mistenkelig med kjøringen, hvis ikke da det å være jævlig god er mistenkelig.