Musharraf, who was president during the murder of Benazir Bhutto, rejected the charges and termed them as politically-motivated, reported Xinhua.
The former president was presented in the court under tight security.
Benazir was assassinated in a suicide attack and firing in Rawalpindi Dec 27, 2007, after she addressed an election campaign rally.
ATC judge Chaudhry Habib-ur-Rehman also indicted six others accused in the case, including two former police officers.
The Federal Investigative Agency (FIA), investigating the murder, had submitted a chargesheet against him in the ATC in the garrison city of Rawalpindi near Islamabad.
The FIA presented a four-point chargesheet against Musharraf in the ATC, accusing him of hatching a conspiracy, in connection with the killing of Benazir Bhutto.
The charge sheet submitted contained the statements of four witnesses, including an American journalist, Mark Siegel, as well as Benazir's own statement.
FIA officials said that the chargesheet has been prepared on the basis of Mark Siegel's statement, who had claimed that Musharraf called and threatened Benazir when he was sitting with her.
Mark Siegel, who once served as lobbyist for Benazir Bhutto in the US, had also stated that Benazir had told him that Musharraf would be responsible for any harm to her.
He had earlier stated that he was with Benazir Bhutto in London when Musharraf denied the allegations.
The chargesheet stated that the statement of the American established Musharraf as the prime accused in Benazir's murder. It also levelled terrorism accusations against the former president. The document stated that Musharraf has failed to prove his innocence in the case.
The ATC had last year summoned Mark Siegel to personally appear in the court and record his statement.
The former president was chargesheeted in Benazir's murder case weeks after Prime Minister Nawaz Sharif announced that high treason case against him would be initiated for abrogating the constitution.
Musharraf was arrested and remanded to judicial custody for a fortnight in June this year over the murder of tribal elder Nawab Akbar Bugti who was killed in military operation in 2006.
He has been kept at his home in Islamabad over security concerns. His house has been declared as a sub-jail.