Former Private Steven Green, 21, wearing baggy shorts and T-shirt, his sandal-clad feet in shackles, appeared briefly in a Kentucky court where he answered "Yes, sir" or "No, sir" to a few questions.
Federal prosecutors said they would ask a grand jury to bring an indictment against him.
He was also granted a public defender because his total assets consisted only of $A8,100 in a cheque account and a 1995 Lincoln Towncar.
Private Green, discharged from the Army with a personality disorder, was charged on June 30 with raping a woman and killing her, her parents and her younger sister in their home in Mahmudiya, Iraq, in March. Other soldiers suspected in the case remain on duty in Iraq.
Scott Wendelsdorf, the public defender, entered a plea of "not guilty on all counts" for Private Green, who was charged with four counts of murder and one count of rape.
He also waived a change of venue and agreed to be prosecuted in Kentucky, home of Fort Campbell, the base of the 101st Airborne to which he was attached before being discharged earlier this year.
An arraignment was set for August 8 and prosecutors said a grand jury would begin considering the case in mid-July.
According to information disclosed by prosecutors earlier Private Green allegedly went to a house near Mahmudiya with three others to rape a woman living there.
After allegedly drinking alcohol and changing into dark clothes, Private Green and others went to the house where he allegedly shot and killed a man, a woman and a five-year-old girl.
He and another person raped a 25-year-old woman who was in the house, and then Green shot her in the head, the charges allege.
Reports from Iraq and the military have given different ages for the girl and the rape victim. The two adults and child were the rape victim's parents and sister, according to a defence official.
Private Green's arrest came amid a series of other investigations in which US troops are suspected of killing civilians in Iraq, including an investigation into the suspected role of US Marines in the killing of 24 unarmed Iraqi civilians in the western town of Haditha last November.