The former Pakistani army chief and president Pervez Musharraf was charged in the 2007 assassination of Benazir Bhutto, according to officials, the AP reported.
Former prime minister Bhutto was killed in 2007 during a rally in the city of Rawalpindi.
"He was charged with murder, criminal conspiracy for murder and facilitation for murder," public prosecutor Chaudhry Azhar said at the anti-terrorism court in Rawalpindi hearing the case Tuesday. Six others were also indicted in Bhutto’s murder, Radio Pakistan reported.
Prosecutors have said Musharraf, who was president at the time, failed to properly protect Bhutto.
Afsha Adil, a member of Musharraf's legal team, said Musharraf pleaded not guilty.
"These charges are baseless. We are not afraid of the proceedings. We will follow legal procedures in the court," Adil said.
Musharraf, 69, has faced a litany of charges relating to his rule since returning to the country in March from self-imposed exile. The four-star general, who came to power in a 1999 bloodless military coup, served as president of Pakistan from 2001 to 2008.
An investigative journalist and academic based in Pakistan, Naveed Ahmad, told Al Jazeera that "Musharraf was the all-powerful man in Pakistan" when Bhutto was murdered.
If Musharraf is convicted, "it will not trigger any political storm," Ahmad said. "The military generals will be upset but without stating it in public at all."
He added that charging Musharraf "ends any prospects of backdoor foreign intervention for his escape from Pakistan on health grounds."
Bhutto, the daughter of former prime minister Zulfikar Ali Bhutto and founder of the Pakistan’s People Party (PPP), survived an attempted coup during her second term as prime minister in 1995. In 1999, Bhutto went into self-imposed exile in Dubai, UAE, after corruption charges were filed against her.
She returned to Pakistan in October 2007, after then-President Musharraf granted her amnesty. Two months later, she was assassinated while leaving a rally.
A large contingent of security forces guarded the area around the court in Rawalpindi, with roads sealed off for Musharraf's appearance.
"He was brought to the courts under very tight security because of the threats from the Tehreek-e-Taliban Pakistan to his life, and then he was immediately rushed back to his farmhouse, which has been turned into a subjail," reported Al Jazeera's Kamal Hyder in Islamabad.
Musharraf's government blamed Bhutto's assassination on Tehreek-e-Taliban Pakistan's chief at the time, Baitullah Mehsud, who denied any involvement. Mehsud was killed in a U.S. drone attack in 2009.
The new government, headed by Nawaz Sharif, whom Musharraf deposed in 1999, has said Musharraf should stand trial for treason for subverting the constitution and has appointed a committee to investigate him.
The offense carries the death penalty or life imprisonment.
Musharraf was arrested after returning from exile to stand in the May elections won by Sharif's party. He was barred from running for parliament because of the legal allegations against him.
He is also wanted for the death of Baloch rebel leader Nawab Akbar Bugti during a military operation in 2006.
Amnesty International has demanded that Pakistan hold Musharraf accountable for all rights violations committed during his rule.
Ehab Zahriyeh contributed to this report. Al Jazeera and wire services