Bonds, 43, repeatedly denied he had knowingly taken performance-enhancing drugs during his December 2003 testimony in an investigation that focused on a San Francisco-area laboratory.
The grand jury in San Francisco returned a five count indictment against Bonds, which includes four counts of perjury and one count of obstruction of justice and accuses him of lying when he said he didn't knowingly take steroids given to him by his personal trainer, Greg Anderson.
The indictment includes the first official public acknowledgement that Bonds allegedly tested positive for steroids and other performance enhancing drugs.
"During the criminal investigation, evidence was obtained including positive tests for the presence of anabolic steroids and other performance-enhancing substances for Bonds and other professional athletes," the indictment said.
Perjury convictions carry possible prison terms of up to five years, while obstruction of justice can bring a 10-year sentence.
Bonds is scheduled to make an initial court appearance December 7, the Justice Department announced.
Shortly after Thursday's indictment, a federal judge released Anderson from prison, said his attorney, Mark Gerragos. After admitting to distributing steroids, Anderson was jailed for refusing to cooperate with prosecutors investigating whether Bonds lied to the grand jury.
"I'm gratified that Greg is walking out," Gerragos said. "However, after reading the indictment there doesn't appear to be anything new. I think keeping him in there for a year was punitive."
In a written statement Thursday, Bonds' attorneys expressed disappointment that "the government did not extend us the courtesy of sharing a copy of the indictment."
"It goes without saying that we look forward to rebutting these unsupported charges in court," said the statement.
Bonds has denied taking steroids at any time in 2001 when he was pursuing the single-season home run record. "During the criminal investigation, evidence was obtained including positive tests for the presence of anabolic steroids and other performance-enhancing substances for Bonds and other athletes," the indictment reads. He is also charged with lying that Anderson never injected him with steroids.
President Bush, a former baseball team owner who has spoken against steroid use, is "very disappointed to hear this," said White House spokesman Tony Fratto. "As this case is now in the criminal justice system, we will refrain from any further specific comments about it. But clearly this is a sad day for baseball."
Bonds was granted immunity for his December 4, 2003, testimony before the grand jury. The indictment states Bonds was promised his testimony would not be used against him except in the cases of "perjury, false declaration or otherwise failing to comply with the court's order."
Bonds filed for free agency last month on the first possible day after the World Series ended with Boston's sweep of the Colorado Rockies -- severing his tenure with San Francisco. Giants owner Peter Magowan told him last month the club would not bring him back for a 16th season.
Bonds, who has hit 762 homers, broke Hank Aaron's record with a shot into the right-center seats off Washington Nationals pitcher Mike Bacsik at San Francisco on August 7. But his achievements on the field have long been shadowed by the drug-use allegations.
He has been selected for 14 All-Star games, a record seven National League Most Valuable Player awards and eight Gold Glove awards.