Clemens faces charges of obstruction of Congress, making false statements and perjury.
The seven-time pitcher of the year told Congress under oath in February 2008 that he had never taken performance-enhancing drugs. He has since been under investigation for lying.
After the indictment, Roger Clemens posted from his verified Twitter account, saying: "I never took HGH or Steroids. And I did not lie to Congress. I look forward to challenging the Governments accusations, and hope people will keep an open mind until trial. I appreciate all the support I have been getting. I am happy to finally have my day in court."
In June, Clemens' former trainer, Brian McNamee, told federal investigators that the seven-time Cy Young Award winner's charitable foundation paid for his training services, which included providing performance-enhancing drugs.
McNamee, who agreed to cooperate to avoid a steroid distribution charge, told authorities the Roger Clemens Foundation paid him from 1998 through 2001, according to several people briefed on the investigation. McNamee, who claims he injected Clemens with steroids, said he was also paid in cash and personal checks.
Clemens’ lawyer, Rusty Hardin disputed McNamee’s claims, saying it is McNamee who is the liar.
"Obviously, Roger never paid him for any drugs anytime and he never paid him out of the foundation for his training services at any time,” Hardin said at the time. "The foundation’s records will show that."
McNamee could not produce documents to support his accusations, according to The New York Times.
Officials stressed that the charges were very serious.
"Whether it's a Member of the Cabinet, a CEO or a professional athlete, if there is evidence that someone has intentionally misled a Congressional investigative Committee, they should be prosecuted to the fullest extent possible," said Kurt Bardella, spokesperson for House Oversight and Government Reform Committee Ranking Member Darrell Issa (R-CA).
"There is no mechanism to justify lying to Congress," he added.