Bolton did not comment to reporters as he entered the courthouse in Greenbelt, Maryland, where he made his initial appearance before a judge on the 18-count indictment brought against him on Thursday.
It's the third criminal case brought in recent weeks by the Justice Department against a Trump adversary.
It is unfolding against the backdrop of growing concerns that the Republican president is using the law enforcement agency to seek retribution against his perceived enemies.
"Now, I have become the latest target in weaponising the Justice Department to charge those he deems to be his enemies," Bolton said in a statement after a grand jury returned the indictment on Thursday.
Bolton is accused of sharing with his wife and daughter more than 1000 pages of notes that included sensitive national defence information he had gleaned from meetings with other US government officials, foreign leaders or from intelligence briefings.
Authorities say some of the information was exposed when operatives believed to be linked to the Iranian government hacked Bolton's email account he used to send the diary-like notes about his activities to his relatives.
Bolton, 76, is a longtime fixture in Republican foreign policy circles who became known for his hawkish views on American power and who served for more than a year in Trump's first administration before being fired in 2019.
He later published a book highly critical of Trump.
While the Bolton investigation burst into public view in August when the FBI searched his home in Maryland and his office in Washington, the inquiry had been well underway by the time Trump took office in January.
Authorities say Bolton took meticulous notes about his meetings and briefings as national security adviser and then used a personal email account and messaging platform to share information classified as high as top secret with his family members.
After sending one document, Bolton wrote in a message to his relatives, "None of which we talk about!!!" In response, one of his relatives wrote, "Shhhhh," prosecutors said.
The indictment also accuses Bolton of storing at his home top secret intelligence about a foreign adversary's plans to attack US forces overseas, covert action taken by the US government or other information authorities say could put the country's national security at risk.
Bolton's attorney, Abbe Lowell, said in a statement that the "underlying facts in this case were investigated and resolved years ago".
He said the charges stem from portions of Bolton's personal diaries over his 45-year career in government and included unclassified information that was shared only with his immediate family and was known to the FBI as far back as 2021.
"Like many public officials throughout history," Lowell said, "Bolton kept diaries — that is not a crime".
He said Bolton "did not unlawfully share or store any information".
Bolton suggested the criminal case was an outgrowth of an unsuccessful Justice Department effort after he left government to block the publication of his 2020 book The Room Where It Happened, which portrayed Trump as grossly misinformed about foreign policy.
The Trump administration asserted that Bolton's manuscript contained classified information that could harm national security if exposed.
Bolton's lawyers have said he moved forward with the book after a White House National Security Council official, with whom Bolton had worked for months, said the manuscript no longer had classified information.
