Daniele Nardello is technically the winner of both the 1999 and 2000 Tour de France’s, as everyone who placed above him (including Lance Armstrong who got 1st in both years) has tested positive for using drugs. He originally placed 7th in 1999 and 10th in 2000.

So Wait, Who Actually Won All Those Tour De France Titles?

In the summer of 2005, I stood on the Champs Élysées feverishly snapping pictures of Lance Armstrong as he ascended the podium erected in the middle of the famous avenue. The Texan had just secured his record seventh and final Tour de France title, assuring that he was the event’s greatest champion. Well, that moment didn’t happen. Sure, I’ve got a photo next to me right now of him with his arms raised in victory as he looks back my way, but that must be my eyes playing tricks on me. Because on Thursday night the US Anti-Doping Agency (USADA) stripped Armstrong of his Tour titles and banned him for life after Lance gave his Chief Joseph impersonation and told the world “he’d fight no more forever.” So who was the champion I should have seen…
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Source: https://www.vice.com/en_us/article/dp4bjk/so-wait-who-actually-won-all-those-tour-de-france-titles