The former Republican security adviser and UN ambassador Bolton is accused of having stored top-secret documents at home and having shared notes with confidential information with relatives.
Bolton appeared in the courtroom in Greenbelt in the state of Maryland, but chose not to answer questions from the reporters waiting outside the court.
The indictment, which includes 18 points, also includes indications that confidential information is alleged to have been exposed when Bolton's email account was hacked by individuals believed to have ties to the Iranian government.
The news that Bolton is being prosecuted came on Thursday. In a statement, he describes himself as a victim of US President Donald Trump's use of the Department of Justice.
"I look forward to fighting to defend my legal actions and exposing his abuse of power", he wrote on Thursday in a statement.
Bolton was security adviser for just over a year and a half during Trump's previous term. In recent years, he has profiled himself as a vocal Trump critic. He has, among other things, called Trump "unfit" as president in a book he wrote after being fired from his position as national security adviser.
Trump has, among other things, taken action against Bolton by revoking his security clearance and withdrawing his personal protection.
