Clemens faces charges of obstruction of Congress, making false statements and perjury.
The former Major League baseball pitcher and his former trainer, Brian McNamee, testified under oath at a 2008 hearing before a House committee and contradicted each other about whether Clemens had used the banned substances.
McNamee has told federal agents, baseball investigator George Mitchell and the committee that he injected Clemens more than a dozen times with steroids and human growth hormone from 1998 to 2001.
Clemens has maintained that McNamee was lying.
Clemens' attorney, Rusty Hardin, said by telephone from Houston that he had just learned of the indictment and would wait to decide whether to comment.
