U.S. District Court Judge Susan Illston ordered prosecutors to amend Bonds' indictment so that each of the five counts against him don't cite multiple statements that prosecutors say are false.
Prosecutors originally accused Bonds of lying 19 different times during his grand jury appearance, and charged him with four counts of perjury and one count of obstruction of justice.
Illston agreed with Bonds' attorney Dennis Riordan that prosecutors must edit out many of the alleged lies or seek a new indictment, which could contain more charges.
Prosecutors are expected to decide whether to seek a new indictment before Bonds' next court date March 21. They declined comment outside court.
Bonds' 2003 grand jury testimony was extensively reported on by the San Francisco Chronicle in December 2004 and in the 2006 book "Game of Shadows," written by the reporters from the original newspaper account. However, Friday was the first time the entire 149-page document was released.
Although the indictment last fall discussed a November 2000 test that showed elevated testosterone and the Chronicle reporters wrote about a November 2001 test that showed an acceptable level, the transcript revealed another sample that previously had not received attention.
A document labeled "BB" with Bonds' date of birth refers to a sample taken in January 2001 for testing by the Bay Area Laboratory Co-Operative, known as BALCO, according to federal prosecutors who questioned Bonds during his three-hour grand jury appearance.
BALCO was the center of a performance-enhancing drug ring. Bonds' personal trainer Greg Anderson, founder Victor Conte and three others pleaded guilty to steroids distribution charges.
In his appearance before the grand jury, Bonds said he didn't understand the results from the January 2001 test prosecutors showed him and then said "that some people may have more testosterone levels than others."
The Chronicle obtained the transcripts from lawyer Troy Ellerman, who was sentenced to two years in prison after he was unmasked as the newspaper's confidential source.
The transcript could bolster each sides' case. In parts, Bonds flatly denies ever taking steroids or human growth hormone, which prosecutors allege are lies.
During the grand jury testimony, prosecutor Jeff Nedrow confronted the slugger with "doping calendars" bearing Bonds' initials and other evidence: "Now, with what you've seen today, do you feel comfortable as you sit here today saying that you have never taken steroids?"
