Appearing before U.S. District Judge Reggie Walton, Clemens, 48, affirmed he understood the charges against him and when the judge asked for his plea, he responded, "Not guilty, your honor," the Houston Chronicle reported.
Pretrial motions were scheduled for March 28 with jury selection to start April 5, the newspaper said.
Prosecutors informed the court they had provided a 34-page index of evidence and 12 computer disks with the material for use by Clemens' lawyers. They also said they would provide all grand jury testimony and FBI interview reports to the defense.
Clemens was to have his mug shot and fingerprints taken inside the federal courthouse.
The seven-time Cy Young Award winner faces charges he lied 2 1/2 years ago to Congress when he testified about steroid use and denied his use of the banned performance-enhancing drug.
Clemens and his wife Debbie were expected to play in the Golf.com World Amateur Handicap Championship in Myrtle Beach, S.C., which started Monday.
Clemens, whose storied career included stints with the New York Yankees, Boston Red Sox, Toronto Blue Jays and Houston Astros, indicated he would fly from Washington to Myrtle Beach to play his round, accompanied by a tournament representative to verify his score, the New York Daily News said. Clemens would rejoin the rest of the field Tuesday.
Clemens was named in an indictment made public last week that said he lied during a congressional hearing when testifying about use of performance-enhancing drugs. The indictment lists one charge of obstruction of Congress, three counts of making false statements and two counts of perjury. If convicted on all counts, Clemens could be sentenced to 30 years in prison and fined $1.5 million.
After the indictment was opened Aug. 19, Clemens posted a statement on Twitter, saying he "never took (human growth hormones) or steroids. And I did not lie to Congress."