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"I've never taken anything in my life, and I never will," said Nadal.
"I'm well enough educated in the sporting world and out of the sporting world to not cheat.
"It's lies and people who write lies are bad people."
Nadal added that he was considering legal action.
Federer will face Mario Ancic in the last eight, a match which has special significance for the world number one as the Croatian seventh seed was the last man to beat him on grass here in 2002.
Since then, Federer has put together a record winning run of 45 matches on his favourite surface, but he is not taking his opponent lightly.
"He's got grass court expertise, it will be a tough match," said the Swiss. Nadal will take on Finland's Jarrko Nieminen who beat Russia's Dmitry Tursunov in a five-set thriller which saw both players hit with a point penalty.
Men's 2002 champion Lleyton Hewitt reached the last eight with a 6-4, 6-4, 4-6, 7-5 win against Spain's David Ferrer and next meets Marcos Baghdatis of Cyprus, the Australian Open runner-up, who knocked out Britain's Andy Murray.