Included in the indictment against Jared Lee Loughner, 22, were charges related to the attempted assassination of Giffords, including the alleged murder of a federal judge, a Giffords assistant and four other individuals.
A source told Raycom News Network that the only time Loughner spoke in court Wednesday was when U.S. District Judge Larry A. Burns asked him if his name was Jared Loughner, to which he replied, "Yes, it is."
At times smiling and nodding his head, Loughner yielded to his attorney when asked how he would plea.
"The attorney voiced the plea," said the source, who had knowledge of the case but was not authorized to speak on the record.
Loughner paid careful attention to prosecutors who spoke during the arraignment, and nodded his head in affirmation when videos were played in court, according to the source.
It is unknown what the videos depicted.
According to the Associated Press (AP), Loughner waded through his appearance "with his arms crossed, head down and eyes closed."
The U.S. Attorney's office in Arizona had asked a judge to order a psychological evaluation of Loughner to determine whether he is mentally sound enough to stand trial.
Voicing his own concerns, Burns sided with the complaint and issued a May 25 competency hearing for Loughner. While more pre-trial activity could come in the meantime, this date is Loughner's next scheduled court appearance.
Loughner, who has been held in federal custody since his Jan. 8 arrest, wore khaki prison closes and sported a new hairdo of "short black hair and side burns," according to the AP.
On Jan. 8, two federal employees, U.S. District Judge Jon M. Roll and Gabe Zimmerman, Giffords' director of community outreach, were killed when Loughner allegedly opened fire, shooting Giffords in the head.
Giffords' 9-year-old constituent, Christina Taylor Green, also was killed, along with Dorothy J. Morris, Phyllis Schneck and Dorwan Stoddard.
The federal indictment includes previous charges brought against Loughner in January.
Additional counts include the use, carry, brandish and discharge of a firearm in relation to a crime of violence; causing death through use of a firearm; and injuring participants at a federally provided activity.
In total, 19 people were shot at Giffords' Congress on Your Corner event at a local Safeway grocery store.
Fourteen of the counts before him are punishable by death. All 49 counts could carry a $250,000 fine, which could total $12.25 million.
Burns is not bound by U.S. sentencing guidelines should Loughner be convicted.
The Pima County Attorney's Office has indicated it will pursue state charges against Loughner.