The indictment, culminating a four-year investigation into steroid use by elite athletes, charged Bonds with four counts of perjury and one of obstruction of justice.
Bonds has steadfastly denied knowingly using any performance enhancing drugs, reports CBS News chief investigative reporter Armen Keteyian. But according to the indictment, "evidence was obtained including positive tests for the presence of anabolic steroids and other performance enhancing substances for Bonds and other athletes."
If Bonds does go to trial, prosecutors would likely also cite "evasive and misleading" testimony before a grand jury in December 2003, where the government contends Bonds lied, under oath, at least 19 times about his use of performance enhancing drugs.
"They're going to focus specifically on what Barry Bonds said and why they think they can prove otherwise," said CBS News legal analyst Andrew Cohen.
If convicted on all five counts, Bonds could go to prison for up to 30 years.
"Every American should worry about a Justice Department that can't tell the difference between prosecution on the one hand, and persecution on the other," Bonds attorney Michael Rains told Keteyian.
The defense has targeted, in particular, the actions of special agent Jeff Novitzky.
CBS News has also learned that in 2004 the government conducted an investigation into whether the agent's credibility would be at issue if the case against Bonds went to trial. To date, the results of that report remain unavailable.
One witness the government won't have is Bonds' former personal trainer. For nearly a year Greg Anderson sat in jail for refusing to discuss, let alone testify against, his longtime friend.
Yesterday, within hours of the indictment, a federal judge ordered him released from prison.
A Major League Record, With Suspicion of An Asterisk
In August, when the 43-year-old Bonds passed Hank Aaron to become baseball's career home run leader, he flatly rejected any suggestion that this milestone was stained by steroids.
"This record is not tainted at all. At all. Period," Bonds said.
Bonds finished the year with 762 homers, seven more than Aaron, and is currently a free agent. In 2001, he set the season record with 73 home runs.
Bonds could not immediately be reached for comment. One of his attorneys, John Burris, didn't know of the indictment before being alerted by The Associated Press and said he would call Bonds to notify him.
"I'm surprised," Burris said, "but there's been an effort to get Barry for a long time. I'm curious what evidence they have now they didn't have before."
Bonds' defense attorney, Mike Rains, declined comment because he hadn't seen a copy of the indictment.
"However, it goes without saying that we look forward to rebutting these unsupported charges in court," Rains said. "We will no doubt have more specific comments in the very near future once we have had the opportunity to actually see this indictment that took so long to generate."
Bonds is scheduled to appear in U.S. District Court in San Francisco on Dec. 7.
Bonds has never been identified by Major League Baseball as testing positive for steroids.
"I have yet to see the details of this indictment and while everyone in America is considered innocent until proven guilty, I take this indictment very seriously and will follow its progress closely," commissioner Bud Selig said.
"However, we must remember, as the U.S. Attorney stated in his press release today, that an indictment contains only allegations, and in this country every defendant, including Barry Bonds, is entitled to the presumption of innocence unless and until such time as he is proven guilty beyond a reasonable doubt."
The White House weighed in, too.
"The president is very disappointed to hear this," Bush spokesman Tony Fratto said. "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."
Mr. Bush, who once owned the Texas Rangers, called Bonds to congratulate him in August when the Giants' outfielder broke the home run mark. "You've always been a great hitter and you broke a great record," Mr. Bush said at the time.
Former Senate Majority Leader George Mitchell, who is investigating drug use in baseball, declined comment. So did Hall of Fame vice president Jeff Idelson.
Bonds was charged in the indictment with lying when he said he didn't knowingly take steroids given to him by Anderson. Bonds is also charged with lying that Anderson never injected him with steroids.
"Greg wouldn't do that," Bonds testified in December 2003 when asked if Anderson ever gave him any drugs that needed to be injected. "He knows I'm against that stuff."
Anderson's attorney, Mark Geragos, said the trainer didn't cooperate with the grand jury that indicted Bonds.
"This indictment came out of left field," Geragos said. "Frankly I'm aghast. It looks like the government misled me and Greg as well, saying this case couldn't go forward without him."
Prosecutors promised Bonds they wouldn't charge him with any drug-related counts if he testified truthfully. But according to the indictment, Bonds repeatedly denied taking any steroids or performance-enhancing drugs despite evidence to the contrary.
For instance, investigators seized a so-called "doping calendar" labeled "BB" during a raid of Anderson's house.
"He could know other BBs," Bonds replied when shown the calendar during his testimony.
Asked directly if Anderson supplied him with steroids, Bonds answered: "Not that I know of." Bonds even denied taking steroids when he was shown documents revealing a positive steroids test for a player named Barry B.
Bonds said at the end of the 2003 season, Anderson rubbed some cream on his arm that the trainer said would help him recover. Anderson also gave him something he called "flax seed oil," Bonds said.
Bonds then testified that prior to the 2003 season, he never took anything supplied by Anderson, which the indictment alleges was a lie because the doping calendars seized from Anderson's house were dated 2001.
Bonds became the highest-profile figure caught up in the government investigation, launched in 2002, with the raid of the Bay Area Laboratory Co-Operative (BALCO), the Burlingame-based supplements lab that was the center of a steroids distribution ring.
Bonds has long been shadowed by allegations that he used performance-enhancing drugs. The son of former big league star Bobby Bonds, Barry broke into the majors with the Pittsburgh Pirates in 1986 as a lithe, base-stealing outfielder.
By the late 1990s, he'd bulked up to more than 240 pounds -- his head, in particular, becoming noticeably bigger. His physical growth was accompanied by a remarkable power surge.
Speculation of his impending indictment had mounted for more than a year.
Bonds' contract with the San Francisco Giants ended this season, adds Keteyian. Now there's a very good reason to believe he may well have played his last game in the major leagues.
Bonds remained out of sight today on a hunting trip.