Twenty one-year-old Dylan Roof pleaded not guilty to the charges against him in the shooting at Emanuel African Methodist Episcopal Church in Charleston, South Carolina, according to the court clerk's office.
The shooting claimed the life of nine people and Roof was indicted on 33 accounts including federal hate crime and firearms charges after the attack which took place earlier this month.
Roof wanted to plead not guilty on all charges, his lawyers said.
The white-supremacist and accused murderer of nine black people during a Bible class at the church, was arrested after his offence, which he reportedly carried out in order to start a “race war,” according to his own statements.
Police said the man intentionally spared some people, so that they could describe what he had done. Survivors include an 11-year-old girl, her grandmother and an elderly trustee of the church.
Survivors also recounted that the man was articulating racist remarks as he carried out the shootings.
Roof has previously appeared in photos waving a Confederate flag and burning the US flag, in his attempt to promote racial violence.
If found guilty of the federal charges, Roof may face life imprisonment or the death penalty while his lawyer, David Bruck, said he would not enter guilty pleas for Roof until the prosecutors announce they would seek the death penalty.