The indictment announced Thursday has only five counts, but includes the most serious charge that Bonds perjured himself to a grand jury in 2003, the San Francisco Chronicle reported. Six counts have been dismissed.
With 762, Bonds holds the major league record for career home runs. But that record and the others he holds have been tainted by his alleged use of steroids.
Bonds has said he believed his trainer, Greg Anderson, was giving him arthritis balm and flaxseed oil in lotions and creams and not steroids or testosterone.
The indictment now includes four counts of perjury and one of obstruction of justice. Prosecutors say Bonds responded to questions before the grand jury with answers that were "intentionally evasive, false and misleading."
The grand jury was investigating the BALCO scandal. BALCO founder Victor Conte, Anderson and three others pleaded guilty, but Anderson refused to testify against Bonds.