Musharraf was driven to the court in Rawalpindi from his plush villa on the outskirts of Islamabad where he is serving a two-week arrest order for other charges dating back to his 1999-2008 rule.
Musharraf faces charges of conspiracy to murder Bhutto, who died in a gun and suicide attack in 2007, one of three cases he is fighting in the courts since returning home last month after four years in self-imposed exile.
On Monday, Pakistan`s caretaker government refused to put Musharraf on a separate trial for treason, telling the Supreme Court that it was beyond its mandate.
Security at the court was tight with journalists barred from entering. Armed police and paramilitary rangers stood alert and blocked all approaches, an AFP reporter said.
About 150 lawyers opposed to Musharraf shouted "dog, dog, Musharraf dog" while about two dozen of Musharraf`s supporters chanted "Long live Musharraf."
He has been threatened with death by the Taliban and barred from running in next month`s general election, a humiliating blow to the man who returned home promising to "save" Pakistan.